JAL-4435 Added coloured dashed lines for secondary structure providers.

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 41e491c..7b632d8 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -3205,7 +3205,7 @@ public class AlignmentUtils
   }
   
   // Method to get the key for a given provider value
-  public static String getProviderKey(String providerValue) {
+  public static String getSecondaryStructureProviderKey(String providerValue) {
       for (Map.Entry<String, String> entry : Constants.STRUCTURE_PROVIDERS.entrySet()) {
           if (entry.getValue().equals(providerValue)) {
               return entry.getKey();  // Return the key (abbreviation) for the matching provider value
@@ -3229,4 +3229,13 @@ public class AlignmentUtils
     
     return reducedLabel; // Return the reduced label if abbreviations were applied
   }
+  
+  public static Color getSecondaryStructureProviderColor(String label) {
+
+    //return Constants.STRUCTURE_PROVIDERS_COLOR.getOrDefault(label, Color.BLACK);
+    Color c =  Constants.STRUCTURE_PROVIDERS_COLOR.get(label.trim());
+    if(c==null)
+      c = Color.BLACK;
+    return c;
+  }
 }
\ No newline at end of file

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 49b569a..c42546c 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import java.awt.BasicStroke;
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Font;
@@ -85,6 +86,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 {
   /** DOCUMENT ME!! */
   public static final String PLACEHOLDER = " * ";
+  
+  private static final int DASHED_LINE_Y_OFFSET = 5;
 
   TreeModel tree;
 
@@ -445,32 +448,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
         nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
       }
+      
       if (node.hasLabel())
       {
-        String label = node.getLabel();
-        
-        if(label.length() > labelLengthThreshold) {
-          
-          //label = AlignmentUtils.reduceLabelLength(label);
-        }
-        
-        nodeLabel = label + " | " + nodeLabel;
-
-        // Split the nodeLabel by "|"
-        String[] lines = nodeLabel.split("\\|");
-
-        // Iterate over the lines and draw each line separately
-        String longestLabelString = "";
-        int i = 0;
-        for (i = 0; i < lines.length; i++) {
-            g.drawString(lines[i].trim(), xstart + 2, ypos - 2 - (i * fm.getHeight()));
-            if(longestLabelString.length() < lines[i].trim().length()) {
-              longestLabelString = lines[i].trim();
-            }
-        }
+        drawLinesAndLabelsForSecondaryStructureProvider(g, node, xstart, xend, ypos, nodeLabel);
         
-        int labelWidth = fm.stringWidth(longestLabelString);
-        int labelHeight = fm.getHeight() * (i-1);
+        int labelWidth = 20;
+        int labelHeight = fm.getHeight();
 
         // Calculate the bounding box of the string
         int xLabelPos = xstart + 2;
@@ -478,7 +462,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         Rectangle labelBounds = new Rectangle(xLabelPos, yLabelPos - labelHeight, labelWidth, labelHeight);
 
         // Add the bounding box to the map for this node (list allows multiple bounding boxes)
-        labelBoundsMap.computeIfAbsent(node, k -> new ArrayList<>()).add(labelBounds);
+        labelBoundsMap.computeIfAbsent(node, k -> new ArrayList<>()).add(labelBounds);        
+        
       }
 
       else if (!nodeLabel.equals(""))
@@ -487,6 +472,73 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       }
     }
   }
+  
+  
+  private void drawLinesAndLabelsForSecondaryStructureProvider(Graphics g, BinaryNode node, 
+          int xstart, int xend, int ypos, String nodeLabel) {
+    // Cast the Graphics object to Graphics2D
+    Graphics2D g2d = (Graphics2D) g.create();
+
+    // Set dash pattern
+    float[] dashPattern = {2, 3};
+    g2d.setStroke(new BasicStroke(
+            1.5f, 
+            BasicStroke.CAP_BUTT,
+            BasicStroke.JOIN_ROUND, 
+            0.0f, 
+            dashPattern, 
+            0.0f));
+
+    String label = node.getLabel();
+    String[] lines = label.split("\\|");
+    
+    int mid = lines.length / 2;
+    
+    // Draw lines for the first half
+    int firstHalfLinesCount = mid;
+
+    drawSecondaryStructureProviderLinesSection(g2d, 
+            lines, 0, mid, xstart, xend, 
+            ypos - DASHED_LINE_Y_OFFSET,
+            true);
+    drawVerticalLineAndLabel(g, xstart, ypos, firstHalfLinesCount, true, nodeLabel); 
+
+    // Draw lines for the second half
+    int secondHalfLinesCount = lines.length - mid;
+    drawSecondaryStructureProviderLinesSection(g2d, 
+            lines, mid, lines.length, xstart, xend, 
+            ypos + DASHED_LINE_Y_OFFSET,
+            false);
+    drawVerticalLineAndLabel(g, xstart, ypos, secondHalfLinesCount, false, nodeLabel); 
+
+    g2d.dispose(); 
+}
+
+  private void drawSecondaryStructureProviderLinesSection(Graphics2D g2d, String[] lines, int start, int end, int xstart, int xend, int baseY, boolean above) {
+      for (int i = start; i < end; i++) {
+          int adjustedY = above 
+                  ? baseY - ((i - start) * DASHED_LINE_Y_OFFSET) 
+                          : baseY +((i - start) * DASHED_LINE_Y_OFFSET);
+          Color providerColor = AlignmentUtils.getSecondaryStructureProviderColor(lines[i]);
+          g2d.setColor(providerColor);
+          g2d.drawLine(xstart, adjustedY, xend, adjustedY);
+      }
+  }
+  
+  private void drawVerticalLineAndLabel(Graphics g, int xstart, int ypos, 
+          int linesCount, boolean above, String nodeLabel) {
+    int adjustedY = above 
+            ? ypos - (linesCount) * DASHED_LINE_Y_OFFSET 
+            : ypos + (linesCount) * DASHED_LINE_Y_OFFSET;
+
+    // Draw vertical line
+    g.drawLine(xstart, ypos, xstart, adjustedY);
+
+    // Draw label
+    if(above && !nodeLabel.equals(""))
+      g.drawString(nodeLabel, xstart + 2, adjustedY - 2);
+}
+
 
   /**
    * DOCUMENT ME!

diff --git a/src/jalview/util/Constants.java b/src/jalview/util/Constants.java
index b8afeeb..b24182c 100644 (file)
--- a/src/jalview/util/Constants.java
+++ b/src/jalview/util/Constants.java
@@ -20,6 +20,7 @@
  */
 package jalview.util;
 
+import java.awt.Color;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -71,4 +72,15 @@ public class Constants
       STRUCTURE_PROVIDERS.put("JP", "JPred");
       STRUCTURE_PROVIDERS.put("AFill", "AlphaFill");
   }
+  
+  public static final Map<String, Color> STRUCTURE_PROVIDERS_COLOR = new HashMap<>();
+
+  static {
+      STRUCTURE_PROVIDERS_COLOR.put("No Secondary Structure", Color.GRAY);
+      STRUCTURE_PROVIDERS_COLOR.put("AlphaFold DB", new Color(255, 0, 0));
+      STRUCTURE_PROVIDERS_COLOR.put("SWISS-MODEL", new Color(255, 165, 0));
+      STRUCTURE_PROVIDERS_COLOR.put("PDB", new Color(0, 128, 0));
+      STRUCTURE_PROVIDERS_COLOR.put("JPred", new Color(0, 0, 255));
+      STRUCTURE_PROVIDERS_COLOR.put("AlphaFill", Color.CYAN);
+  }
 }