ported logo rendering and label fit to column width - but disabled due to 1.1 incompa...

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 38e0331..c5da18b 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -22,8 +22,8 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import jalview.datamodel.*;
+import jalview.schemes.ColourSchemeI;
 
 public class AnnotationPanel extends Panel implements AdjustmentListener,
         ActionListener, MouseListener, MouseMotionListener
@@ -566,7 +566,8 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
    */
   public void drawComponent(Graphics g, int startRes, int endRes)
   {
-    g.setFont(av.getFont());
+    Font ofont = av.getFont();
+    g.setFont(ofont);
 
     g.setColor(Color.white);
     g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
@@ -600,8 +601,12 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
     int iconOffset = av.charHeight / 2;
     boolean validRes = false;
     boolean validEnd = false;
+    boolean labelAllCols = false;
+    boolean centreColLabels,centreColLabelsDef = av.getCentreColumnLabels();
+    boolean scaleColLabel=false;
     boolean[] graphGroupDrawn = new boolean[aa.length];
-
+    int charOffset = 0; // offset for a label
+    float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a column.
     // \u03B2 \u03B1
     for (int i = 0; i < aa.length; i++)
     {
@@ -611,7 +616,9 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
       {
         continue;
       }
-
+      centreColLabels = row.centreColLabels || centreColLabelsDef;
+      labelAllCols = row.showAllColLabels;
+      scaleColLabel = row.scaleColLabel;
       lastSS = ' ';
       lastSSX = 0;
 
@@ -627,13 +634,15 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
 
         if (row.hasText)
         {
+          iconOffset = av.charHeight - fm.getDescent();
           y -= av.charHeight;
         }
       }
-
-      if (row.hasText)
+      //TODO: else is the logic used in application, applet had no 'else'
+      else if (row.hasText)
       {
-        iconOffset = av.charHeight / 2;
+        iconOffset = av.charHeight - fm.getDescent();
+
       }
       else
       {
@@ -692,14 +701,31 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
                 && (row.annotations[column].displayCharacter != null && row.annotations[column].displayCharacter
                         .length() > 0))
         {
-          int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth - fm
-                  .charsWidth(row.annotations[column].displayCharacter
-                          .toCharArray(), 0,
-                          row.annotations[column].displayCharacter.length())) / 2)
-                  : (av.charWidth - fm
-                          .charWidth(row.annotations[column].displayCharacter
-                                  .charAt(0))) / 2;
-
+                  
+          if (centreColLabels || scaleColLabel)
+          {
+            fmWidth = (float) fm
+            .charsWidth(row.annotations[column].displayCharacter
+                    .toCharArray(), 0,
+                    row.annotations[column].displayCharacter.length());
+
+            if ( scaleColLabel ) { 
+              // justify the label and scale to fit in column
+              if (fmWidth > av.charWidth) {
+                // scale only if the current font isn't already small enough
+                fmScaling = av.charWidth;
+                fmScaling /= fmWidth;
+                // not 1.1 // g.setFont(new Font(ofont,AffineTransform.getScaleInstance(fmScaling, 1.0)));
+                // and update the label's width to reflect the scaling.
+                fmWidth = av.charWidth;
+              }
+            }
+          } else {
+            fmWidth = (float) fm
+            .charWidth(row.annotations[column].displayCharacter.charAt(0));
+          }
+          charOffset =  (int) ((av.charWidth - fmWidth) / 2f);
+          
           if (row.annotations[column].colour == null)
             g.setColor(Color.black);
           else
@@ -708,16 +734,17 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
           if (column == 0 || row.graph > 0)
           {
             g.drawString(row.annotations[column].displayCharacter,
-                    (x * av.charWidth) + charOffset, y + iconOffset + 3);
+                    (x * av.charWidth) + charOffset, y + iconOffset + 3); // + 3?
           }
           else if (row.annotations[column - 1] == null
-                  || (!row.annotations[column].displayCharacter
+                  || (labelAllCols||!row.annotations[column].displayCharacter
                           .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
                           .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
           {
             g.drawString(row.annotations[column].displayCharacter,
-                    (x * av.charWidth) + charOffset, y + iconOffset + 3);
+                    (x * av.charWidth) + charOffset, y + iconOffset + 3); // +3?
           }
+          g.setFont(ofont);
         }
 
         if (row.hasIcons)
@@ -1037,11 +1064,16 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
   public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
           int eRes, float min, float max, int y)
   {
+    ColourSchemeI profcolour = av.getGlobalColourScheme();
+    if (profcolour==null)
+    {
+      profcolour = new jalview.schemes.ZappoColourScheme();
+    }
     if (sRes > aa.annotations.length)
     {
       return;
     }
-
+    Font ofont = g.getFont();
     eRes = Math.min(eRes, aa.annotations.length);
 
     int x = 0, y1 = y, y2 = y;
@@ -1059,7 +1091,19 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
 
     int column;
     int aaMax = aa.annotations.length - 1;
-
+    boolean renderHistogram = true, renderProfile = false;
+    /* Logos are disabled for 2.5 release : Bug # 0060064
+     * if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
+      // TODO: generalise this to have render styles for consensus/profile data 
+      if (aa.groupRef!=null)
+      {
+        renderHistogram = aa.groupRef.isShowConsensusHistogram();
+        renderProfile = aa.groupRef.isShowSequenceLogo();
+      } else {
+        renderHistogram = av.isShowConsensusHistogram();
+        renderProfile = av.isShowSequenceLogo();
+      }
+    }*/
     while (x < eRes - sRes)
     {
       column = sRes + x;
@@ -1087,6 +1131,8 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
       y1 = y
               - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
 
+      if (renderHistogram)
+      {      
       if (y1 - y2 > 0)
       {
         g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
@@ -1095,7 +1141,40 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
       {
         g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
       }
+      }
+      // draw profile if available
+      // Disabled for 2.5 release: see bug #0060064
+      /**
+      if (aa.annotations[column].value!=0 && renderProfile)
+      {
+        int profl[] = getProfileFor(aa,column);
+        int ht = y1; //,htn=y2-y1;//aa.graphHeight;
+          float wdth;
+          double ht2=0;
+          char[] dc = new char[1];
+          // LineMetrics lm;
+          for (int c=1;profl!=null && c<profl[0];)
+          {
+            dc[0] = (char) profl[c++];
+            wdth = av.charWidth;
+            wdth/=(float) fm
+                    .charsWidth(dc,0,1);
 
+            if (c>2)
+            {
+              ht+=(int)ht2;
+            }
+            {
+              // not java 1.1 compatible: Bug # 0060064
+              g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, (ht2=(htn*((double)profl[c++])/100.0))/av.charHeight)));
+              lm = g.getFontMetrics().getLineMetrics(dc,0,1, g);
+              g.setColor(profcolour.findColour(dc[0]));
+              g.drawChars(dc,0,1,x*av.charWidth, (int) (ht+lm.getHeight())); 
+            }
+          }
+          g.setFont(ofont);
+      }
+      **/
       x++;
 
     }
@@ -1107,6 +1186,24 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
     }
   }
 
+  /*
+   * Disabled for 2.5 release - see bug #0060064
+  private int[] getProfileFor(AlignmentAnnotation aa, int column)
+  {
+//    if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
+    if (aa.groupRef!=null && aa.groupRef.consensusData!=null) { // && aa.groupRef.isShowSequenceLogo()) {
+      return AAFrequency.extractProfile(aa.groupRef.consensusData[column],aa.groupRef.getIgnoreGapsConsensus());
+    }
+    // TODO extend annotation row to enable dynamic and static profile data to be stored  
+    if (aa.groupRef==null && aa.sequenceRef==null) //  && av.isShowSequenceLogo())
+    {
+      return AAFrequency.extractProfile(av.hconsensus[column],av.getIgnoreGapsConsensus());
+    }
+  //  }
+    return null;
+  }
+   */
+
   // used by overview window
   public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
           int y, int sRes, int eRes)