diff --git a/.idea/uiDesigner.xml b/.idea/uiDesigner.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e96534fb27b68192f27f985d3879e173ec77adb8
--- /dev/null
+++ b/.idea/uiDesigner.xml
@@ -0,0 +1,124 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="Palette2">
+ <group name="Swing">
+ <item class="com.intellij.uiDesigner.HSpacer" tooltip-text="Horizontal Spacer" icon="/com/intellij/uiDesigner/icons/hspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
+ <default-constraints vsize-policy="1" hsize-policy="6" anchor="0" fill="1" />
+ </item>
+ <item class="com.intellij.uiDesigner.VSpacer" tooltip-text="Vertical Spacer" icon="/com/intellij/uiDesigner/icons/vspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
+ <default-constraints vsize-policy="6" hsize-policy="1" anchor="0" fill="2" />
+ </item>
+ <item class="javax.swing.JPanel" icon="/com/intellij/uiDesigner/icons/panel.png" removable="false" auto-create-binding="false" can-attach-label="false">
+ <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3" />
+ </item>
+ <item class="javax.swing.JScrollPane" icon="/com/intellij/uiDesigner/icons/scrollPane.png" removable="false" auto-create-binding="false" can-attach-label="true">
+ <default-constraints vsize-policy="7" hsize-policy="7" anchor="0" fill="3" />
+ </item>
+ <item class="javax.swing.JButton" icon="/com/intellij/uiDesigner/icons/button.png" removable="false" auto-create-binding="true" can-attach-label="false">
+ <default-constraints vsize-policy="0" hsize-policy="3" anchor="0" fill="1" />
+ <initial-values>
+ <property name="text" value="Button" />
+ </initial-values>
+ </item>
+ <item class="javax.swing.JRadioButton" icon="/com/intellij/uiDesigner/icons/radioButton.png" removable="false" auto-create-binding="true" can-attach-label="false">
+ <default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
+ <initial-values>
+ <property name="text" value="RadioButton" />
+ </initial-values>
+ </item>
+ <item class="javax.swing.JCheckBox" icon="/com/intellij/uiDesigner/icons/checkBox.png" removable="false" auto-create-binding="true" can-attach-label="false">
+ <default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
+ <initial-values>
+ <property name="text" value="CheckBox" />
+ </initial-values>
+ </item>
+ <item class="javax.swing.JLabel" icon="/com/intellij/uiDesigner/icons/label.png" removable="false" auto-create-binding="false" can-attach-label="false">
+ <default-constraints vsize-policy="0" hsize-policy="0" anchor="8" fill="0" />
+ <initial-values>
+ <property name="text" value="Label" />
+ </initial-values>
+ </item>
+ <item class="javax.swing.JTextField" icon="/com/intellij/uiDesigner/icons/textField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+ <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+ <preferred-size width="150" height="-1" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JPasswordField" icon="/com/intellij/uiDesigner/icons/passwordField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+ <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+ <preferred-size width="150" height="-1" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JFormattedTextField" icon="/com/intellij/uiDesigner/icons/formattedTextField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+ <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+ <preferred-size width="150" height="-1" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JTextArea" icon="/com/intellij/uiDesigner/icons/textArea.png" removable="false" auto-create-binding="true" can-attach-label="true">
+ <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+ <preferred-size width="150" height="50" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JTextPane" icon="/com/intellij/uiDesigner/icons/textPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
+ <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+ <preferred-size width="150" height="50" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JEditorPane" icon="/com/intellij/uiDesigner/icons/editorPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
+ <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+ <preferred-size width="150" height="50" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JComboBox" icon="/com/intellij/uiDesigner/icons/comboBox.png" removable="false" auto-create-binding="true" can-attach-label="true">
+ <default-constraints vsize-policy="0" hsize-policy="2" anchor="8" fill="1" />
+ </item>
+ <item class="javax.swing.JTable" icon="/com/intellij/uiDesigner/icons/table.png" removable="false" auto-create-binding="true" can-attach-label="false">
+ <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+ <preferred-size width="150" height="50" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JList" icon="/com/intellij/uiDesigner/icons/list.png" removable="false" auto-create-binding="true" can-attach-label="false">
+ <default-constraints vsize-policy="6" hsize-policy="2" anchor="0" fill="3">
+ <preferred-size width="150" height="50" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JTree" icon="/com/intellij/uiDesigner/icons/tree.png" removable="false" auto-create-binding="true" can-attach-label="false">
+ <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+ <preferred-size width="150" height="50" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JTabbedPane" icon="/com/intellij/uiDesigner/icons/tabbedPane.png" removable="false" auto-create-binding="true" can-attach-label="false">
+ <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3">
+ <preferred-size width="200" height="200" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JSplitPane" icon="/com/intellij/uiDesigner/icons/splitPane.png" removable="false" auto-create-binding="false" can-attach-label="false">
+ <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3">
+ <preferred-size width="200" height="200" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JSpinner" icon="/com/intellij/uiDesigner/icons/spinner.png" removable="false" auto-create-binding="true" can-attach-label="true">
+ <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
+ </item>
+ <item class="javax.swing.JSlider" icon="/com/intellij/uiDesigner/icons/slider.png" removable="false" auto-create-binding="true" can-attach-label="false">
+ <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
+ </item>
+ <item class="javax.swing.JSeparator" icon="/com/intellij/uiDesigner/icons/separator.png" removable="false" auto-create-binding="false" can-attach-label="false">
+ <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3" />
+ </item>
+ <item class="javax.swing.JProgressBar" icon="/com/intellij/uiDesigner/icons/progressbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
+ <default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1" />
+ </item>
+ <item class="javax.swing.JToolBar" icon="/com/intellij/uiDesigner/icons/toolbar.png" removable="false" auto-create-binding="false" can-attach-label="false">
+ <default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1">
+ <preferred-size width="-1" height="20" />
+ </default-constraints>
+ </item>
+ <item class="javax.swing.JToolBar$Separator" icon="/com/intellij/uiDesigner/icons/toolbarSeparator.png" removable="false" auto-create-binding="false" can-attach-label="false">
+ <default-constraints vsize-policy="0" hsize-policy="0" anchor="0" fill="1" />
+ </item>
+ <item class="javax.swing.JScrollBar" icon="/com/intellij/uiDesigner/icons/scrollbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
+ <default-constraints vsize-policy="6" hsize-policy="0" anchor="0" fill="2" />
+ </item>
+ </group>
+ </component>
+</project>
\ No newline at end of file
diff --git a/src/main/java/Canidate.java b/src/main/java/Canidate.java
index 63ae1f7533ff89381084e00d150406f9bdd65152..1afb4853bee40bf001ab608e7514f111c570940b 100644
--- a/src/main/java/Canidate.java
+++ b/src/main/java/Canidate.java
@@ -40,7 +40,7 @@ public class Canidate {
return vertexList;
}
- public double calculateFitness(boolean doOutput) {
+ public double[] calculateFitness(boolean doOutput) {
double fitness = 0d;
int hydrophobicBonds = calculateBonds();
@@ -53,7 +53,7 @@ public class Canidate {
+ " [hydrophobicBonds = " + hydrophobicBonds + " | overlaps = " + overlaps + "]\n");
}
- return fitness;
+ return new double[]{fitness, hydrophobicBonds, overlaps};
}
public ArrayList<Vertex> getVertexList() {
diff --git a/src/main/java/GraphicsExample.java b/src/main/java/GraphicsExample.java
deleted file mode 100644
index 1f6c2dd2dc21c106e969a70f25890f92e9882e2a..0000000000000000000000000000000000000000
--- a/src/main/java/GraphicsExample.java
+++ /dev/null
@@ -1,69 +0,0 @@
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
-import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.IOException;
-
-import javax.imageio.ImageIO;
-
-
-// Example to illustrate Java 2D graphics usage for Genetic Algorithms
-// (C) Alexander del Pino
-
-public class GraphicsExample {
-
-
-
- public static void main(String[] args) {
-
- int height = 500;
- int width = 800;
-
- BufferedImage image = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
- Graphics2D g2 = image.createGraphics();
- g2.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
-
- g2.setColor(Color.YELLOW);
- g2.fillRect(0, 0, width, height);
-
- int cellSize = 80;
-
- g2.setColor(new Color(0, 200, 0));
- g2.fillRect(50, 50, cellSize, cellSize);
-
- g2.setColor(new Color(255, 0, 0));
- g2.fillRect(250, 50, cellSize, cellSize);
-
- g2.setColor(Color.BLACK);
- g2.drawLine(50 + cellSize, 50+cellSize/2, 250, 50+cellSize/2);
-
- g2.setColor(new Color(255, 255, 255));
- String label = "GA";
- Font font = new Font("Serif", Font.PLAIN, 40);
- g2.setFont(font);
- FontMetrics metrics = g2.getFontMetrics();
- int ascent = metrics.getAscent();
- int labelWidth = metrics.stringWidth(label);
-
- g2.drawString(label, 50 + cellSize/2 - labelWidth/2 , 50 + cellSize/2 + ascent/2);
-
- String folder = "./visualization/individual/";
- String filename = "image.png";
- if (!new File(folder).exists()) new File(folder).mkdirs();
-
- try {
- ImageIO.write(image, "png", new File(folder + File.separator + filename));
- } catch (IOException e) {
- e.printStackTrace();
- System.exit(0);
- }
-
-
-
- }
-
-
-}
diff --git a/src/main/java/Main.java b/src/main/java/Main.java
index 8abc3795e3bb5c9990e7b68bb6b75d06030035ba..b7492c15b9db4d195bad5a8cefd722993e59d3e0 100644
--- a/src/main/java/Main.java
+++ b/src/main/java/Main.java
@@ -9,38 +9,39 @@ public class Main {
ProteinDrawer pdraw = new ProteinDrawer("./visualization/individual/", "image.png");
- int[] isHydrophobic = {0, 0, 0, 1, 0, 1, 1, 0, 1}; // 0 = no | 1 = yes
+ int[] isHydrophobic = {0, 0, 0, 1, 0, 1, 1, 0, 0}; // 0 = no | 1 = yes
// Last outgoing direction has no influence on the protein
int[] outgoingDirection = {0, 1, 2, 1, 2, 3, 3, 1, 0}; // 0 = North | 1 = East | 2 = South | 3 = West
Canidate c = new Canidate(isHydrophobic, outgoingDirection);
- c.calculateFitness(true);
+ double[] fitnessBondOverlap = c.calculateFitness(true);
pdraw.printProtein(c.getVertexList());
-
- Random rd = new Random();
- int proteinSize = 20;
- int[] isHydrophobicRandom = new int[proteinSize];
- int[] outgoingDirectionRandom = new int[proteinSize];
-
- for (int i = 0; i < proteinSize; i++) {
- isHydrophobicRandom[i] = rd.nextInt(2);
- outgoingDirectionRandom[i] = rd.nextInt(4);
- }
-
- System.out.print("Hydrophobic: ");
- for (int a : isHydrophobicRandom) {
- System.out.print(a + " ");
- }
- System.out.println();
-
- System.out.print("Outgoing Direction: ");
- for (int a : outgoingDirectionRandom) {
- System.out.print(a + " ");
- }
-
- System.out.println();
- Canidate cRandom = new Canidate(isHydrophobicRandom, outgoingDirectionRandom);
- cRandom.calculateFitness(true);
- pdraw.printProtein(cRandom.getVertexList());
+ pdraw.drawProteinToFile(c.getVertexList(), fitnessBondOverlap);
+
+// Random rd = new Random();
+// int proteinSize = 20;
+// int[] isHydrophobicRandom = new int[proteinSize];
+// int[] outgoingDirectionRandom = new int[proteinSize];
+//
+// for (int i = 0; i < proteinSize; i++) {
+// isHydrophobicRandom[i] = rd.nextInt(2);
+// outgoingDirectionRandom[i] = rd.nextInt(4);
+// }
+//
+// System.out.print("Hydrophobic: ");
+// for (int a : isHydrophobicRandom) {
+// System.out.print(a + " ");
+// }
+// System.out.println();
+//
+// System.out.print("Outgoing Direction: ");
+// for (int a : outgoingDirectionRandom) {
+// System.out.print(a + " ");
+// }
+//
+// System.out.println();
+// Canidate cRandom = new Canidate(isHydrophobicRandom, outgoingDirectionRandom);
+// cRandom.calculateFitness(true);
+// pdraw.printProtein(cRandom.getVertexList());
}
}
diff --git a/src/main/java/ProteinDrawer.java b/src/main/java/ProteinDrawer.java
index 576f88324ab9a166175ed7ba72fbac37a55d5eb5..9ee6f1d9b306b7aeb14ffdb808044203f832785f 100644
--- a/src/main/java/ProteinDrawer.java
+++ b/src/main/java/ProteinDrawer.java
@@ -1,3 +1,8 @@
+import javax.imageio.ImageIO;
+import java.awt.*;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
@@ -8,41 +13,141 @@ public class ProteinDrawer {
// Used only for the console output
String consoleEmpty = " ";
- String consoleHydrophobic = " o ";
- String consoleHydrophilic = " i ";
- String consoleMultiple = " z ";
+ String consoleHydrophobic = "(o)";
+ String consoleHydrophilic = "(i)";
+ String consoleHydrophobicMulti = "{o}";
+ String consoleHydrophilicMulti = "{i}";
+ String consoleMixed = "{z}";
String consoleConnectionVertical = " | ";
String consoleConnectionHorizontal = "---";
+ // For image
+ int pixelsPerCell = 40;
+ int margin = pixelsPerCell * 2;
+ int outline = 2;
+ Font font = new Font("Sans-Serif", Font.PLAIN, 15);
+ Color imageBackground = new Color(255, 255, 255);
+ Color imageConnection = new Color(0, 0, 0);
+ Color imageOutline = new Color(0, 0, 0);
+ Color imageHydrophobic = new Color(205, 0, 0);
+ Color imageHydrophilic = new Color(0, 0, 255);
+ Color imageMixed = new Color(205, 0, 205);
+ Color imageAminoText = new Color(200, 200, 200);
+ Color imageText = new Color(0,0,0);
+
public ProteinDrawer(String folder, String filename) {
this.folder = folder;
this.filename = filename;
}
- public void drawProteinToFile(ArrayList<Vertex> vertexListOriginal) {
+ public void drawProteinToFile(ArrayList<Vertex> vertexListOriginal, double[] fitBondOver) {
// Copy VertexList to be able to manipulate it
ArrayList<Vertex> vertexList = deepCopyVertexList(vertexListOriginal);
- Block[][] proteinArray = convertProteinTo2DArray(vertexList);
+ Cell[][] cellArray = convertProteinTo2DArray(vertexList);
+
+ int height = (cellArray.length * pixelsPerCell) + margin * 2;
+ int width = (cellArray[0].length * pixelsPerCell) + margin * 2;
+
+ BufferedImage image = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+ Graphics2D g2 = image.createGraphics();
+ g2.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
+ g2.setFont(font);
+ FontMetrics metrics = g2.getFontMetrics();
+ int ascent = metrics.getAscent();
+
+ // Background
+ g2.setColor(imageBackground);
+ g2.fillRect(0, 0, width, height);
+
+ for (int yIndex = cellArray.length-1; yIndex >= 0; yIndex--) {
+ int yIndexPosition = cellArray.length-1 - yIndex;
+
+ for (int xIndex = 0; xIndex < cellArray[0].length; xIndex++) {
+ Color aminoColor = null;
+
+ State cellState = cellArray[yIndex][xIndex].getRelevantDrawState();
+
+ switch (cellState) {
+ case Empty:
+ break;
+
+ case Hydrophobic:
+ aminoColor = imageHydrophobic;
+ break;
- for (int yIndex = proteinArray.length-1; yIndex >= 0; yIndex--) {
- for (int xIndex = 0; xIndex < proteinArray[0].length; xIndex++) {
- System.out.print(convertBlockToString(proteinArray[yIndex][xIndex]));
+ case Hydrophilic:
+ aminoColor = imageHydrophilic;
+ break;
+
+ case Mixed:
+ aminoColor = imageMixed;
+ break;
+
+ case ConnectionVertical:
+ g2.setColor(imageConnection);
+ g2.fillRect((xIndex * pixelsPerCell) + margin + (pixelsPerCell/2)-outline,
+ (yIndexPosition * pixelsPerCell) + margin,
+ outline * 2, pixelsPerCell);
+ break;
+
+ case ConnectionHorizontal:
+ g2.setColor(imageConnection);
+ g2.fillRect((xIndex * pixelsPerCell) + margin,
+ (yIndexPosition * pixelsPerCell) + margin + (pixelsPerCell/2)-outline,
+ pixelsPerCell, outline * 2);
+ break;
+ }
+
+ if (aminoColor != null) {
+ g2.setColor(imageOutline);
+ g2.fillRect((xIndex * pixelsPerCell) + margin, (yIndexPosition * pixelsPerCell) + margin,
+ pixelsPerCell, pixelsPerCell);
+ g2.setColor(aminoColor);
+ g2.fillRect((xIndex * pixelsPerCell) + outline + margin, (yIndexPosition * pixelsPerCell) + outline + margin,
+ pixelsPerCell - (outline * 2), pixelsPerCell - (outline * 2));
+
+ g2.setColor(imageAminoText);
+ String label = "";
+ for (int aminoIndex : cellArray[yIndex][xIndex].aminoIndexes) {
+ label += aminoIndex + " ";
+ }
+ int labelWidth = metrics.stringWidth(label);
+ int x = (xIndex * pixelsPerCell) + margin + (pixelsPerCell/2) - (labelWidth/2) + outline;
+ int y = (yIndexPosition * pixelsPerCell) + margin + (pixelsPerCell/2) + (ascent/2) - outline;
+ g2.drawString(label, x, y);
+ }
}
- System.out.println();
}
- System.out.println();
+
+ g2.setColor(imageText);
+ String label = "Fitness: " + fitBondOver[0]
+ + " H/H Bonds: " + (int)fitBondOver[1]
+ + " Overlaps: " + (int)fitBondOver[2];
+ int labelWidth = metrics.stringWidth(label);
+ int x = margin / 4;
+ int y = margin / 4;
+ g2.drawString(label, x, y);
+
+ if (!new File(folder).exists()) new File(folder).mkdirs();
+
+ try {
+ ImageIO.write(image, "png", new File(folder + File.separator + filename));
+ } catch (IOException e) {
+ e.printStackTrace();
+ System.exit(0);
+ }
}
public void printProtein(ArrayList<Vertex> vertexListOriginal) {
// Copy VertexList to be able to manipulate it
ArrayList<Vertex> vertexList = deepCopyVertexList(vertexListOriginal);
- Block[][] proteinArray = convertProteinTo2DArray(vertexList);
+ Cell[][] cellArray = convertProteinTo2DArray(vertexList);
- for (int yIndex = proteinArray.length-1; yIndex >= 0; yIndex--) {
- for (int xIndex = 0; xIndex < proteinArray[0].length; xIndex++) {
- System.out.print(convertBlockToString(proteinArray[yIndex][xIndex]));
+ for (int yIndex = cellArray.length-1; yIndex >= 0; yIndex--) {
+ for (int xIndex = 0; xIndex < cellArray[0].length; xIndex++) {
+ System.out.print(convertCellToString(cellArray[yIndex][xIndex]));
}
System.out.println();
}
@@ -58,7 +163,7 @@ public class ProteinDrawer {
return vertexList;
}
- private Block[][] convertProteinTo2DArray(ArrayList<Vertex> vertexList) {
+ private Cell[][] convertProteinTo2DArray(ArrayList<Vertex> vertexList) {
// Determine size
int minX = 0;
int maxX = 0;
@@ -90,69 +195,68 @@ public class ProteinDrawer {
}
// Add vertexes and connections to 2d array
- Block[][] proteinArray = new Block[maxY * 2 + 1][maxX * 2 + 1];
+ Cell[][] cellArray = new Cell[maxY * 2 + 1][maxX * 2 + 1];
for (int yIndex = 0; yIndex < maxY * 2 + 1; yIndex++) {
for (int xIndex = 0; xIndex < maxX * 2 + 1; xIndex++) {
- proteinArray[yIndex][xIndex] = new Block();
+ cellArray[yIndex][xIndex] = new Cell();
}
}
for (int i = 0; i < vertexList.size(); i++) {
Vertex vertex = vertexList.get(i);
if (vertex.isHydrophobic) {
- proteinArray[vertex.y][vertex.x].addState(State.Hydrophobic);
+ cellArray[vertex.y][vertex.x].addState(State.Hydrophobic);
} else {
- proteinArray[vertex.y][vertex.x].addState(State.Hydrophilic);
+ cellArray[vertex.y][vertex.x].addState(State.Hydrophilic);
}
+ cellArray[vertex.y][vertex.x].addAminoIndex(i);
// Add connection, except on the last one
if (i + 1 != vertexList.size()) {
if (vertex.outgoingDirection == 0) {
- proteinArray[vertex.y + 1][vertex.x].addState(State.ConnectionVertical);
+ cellArray[vertex.y + 1][vertex.x].addState(State.ConnectionVertical);
} else if (vertex.outgoingDirection == 1) {
- proteinArray[vertex.y][vertex.x + 1].addState(State.ConnectionHorizontal);
+ cellArray[vertex.y][vertex.x + 1].addState(State.ConnectionHorizontal);
} else if (vertex.outgoingDirection == 2) {
- proteinArray[vertex.y - 1][vertex.x].addState(State.ConnectionVertical);
+ cellArray[vertex.y - 1][vertex.x].addState(State.ConnectionVertical);
} else if (vertex.outgoingDirection == 3) {
- proteinArray[vertex.y][vertex.x - 1].addState(State.ConnectionHorizontal);
+ cellArray[vertex.y][vertex.x - 1].addState(State.ConnectionHorizontal);
}
}
}
- return proteinArray;
+ return cellArray;
}
- private String convertBlockToString (Block block) {
- boolean multiple = false;
- if (block.states.size() > 1) {
- multiple = true;
- }
+ private String convertCellToString(Cell cell) {
- State blockState = block.states.get(0);
+ State cellState = cell.getRelevantDrawState ();
- switch (blockState) {
+ switch (cellState) {
case Empty:
return consoleEmpty;
case Hydrophobic:
- if (multiple) {
- return consoleMultiple;
- } else {
return consoleHydrophobic;
- }
case Hydrophilic:
- if (multiple) {
- return consoleMultiple;
- } else {
return consoleHydrophilic;
- }
+
+ case HydrophobicMulti:
+ return consoleHydrophobicMulti;
+
+ case HydrophilicMulti:
+ return consoleHydrophilicMulti;
+
+ case Mixed:
+ return consoleMixed;
case ConnectionVertical:
return consoleConnectionVertical;
case ConnectionHorizontal:
return consoleConnectionHorizontal;
+
}
// Fallback
return consoleEmpty;
@@ -175,10 +279,11 @@ public class ProteinDrawer {
}
}
-class Block {
+class Cell {
ArrayList<State> states = new ArrayList<>();
+ ArrayList<Integer> aminoIndexes = new ArrayList<>();
- public Block () {
+ public Cell() {
states.add(State.Empty);
}
@@ -188,12 +293,42 @@ class Block {
}
states.add(state);
}
+
+ public void addAminoIndex (int aminoIndex) {
+ aminoIndexes.add(aminoIndex);
+ }
+
+ public State getRelevantDrawState () {
+ State rc = states.get(0);
+ if (states.size() > 1) {
+ if (rc.equals(State.Hydrophobic)) {
+ for (State s : states) {
+ if (s.equals(State.Hydrophilic)) {
+ return State.Mixed;
+ }
+ }
+ return State.HydrophobicMulti;
+
+ } else if (rc.equals(State.Hydrophilic)) {
+ for (State s : states) {
+ if (s.equals(State.Hydrophobic)) {
+ return State.Mixed;
+ }
+ }
+ return State.HydrophilicMulti;
+ }
+ }
+ return rc;
+ }
}
enum State {
Empty,
Hydrophobic,
Hydrophilic,
+ HydrophobicMulti,
+ HydrophilicMulti,
+ Mixed,
ConnectionVertical,
ConnectionHorizontal
}
\ No newline at end of file