X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=b2a5ede4432814a78eb35cc665fddb58ab85c9be;hb=0fc704a18faa7d11b6d02876bb6c1e8bc19f343c;hp=1f91e26be49b5af5c4143b30e1c647b0c812abf1;hpb=f3bc67915e61855d87866b4a614fe7a953813408;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 1f91e26..b2a5ede 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -43,6 +43,9 @@ public class IdCanvas extends JPanel
     int imgHeight = 0;
     boolean fastPaint = false;
     java.util.Vector searchResults;
+    FontMetrics fm;
+    AnnotationLabels labels = null;
+    AnnotationPanel ap;
 
     /**
      * Creates a new IdCanvas object.
@@ -67,6 +70,8 @@ public class IdCanvas extends JPanel
      */
     public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, int ypos)
     {
+        int xPos = 0;
+        int panelWidth = getWidth();
         int charHeight = av.charHeight;
 
         if ((searchResults != null) && searchResults.contains(s))
@@ -86,15 +91,21 @@ public class IdCanvas extends JPanel
         }
         else
         {
-            gg.setColor(s.getColor());
+            gg.setColor(av.getSequenceColour(s));
             gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
                 charHeight);
             gg.setColor(Color.black);
         }
 
+        if (av.rightAlignIds)
+        {
+          xPos = panelWidth - fm.stringWidth(
+              s.getDisplayId(av.getShowJVSuffix())
+              ) - 4;
+        }
 
         gg.drawString( s.getDisplayId(av.getShowJVSuffix()),
-                      0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+                    xPos, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
 
         if (av.hasHiddenRows && av.showHiddenMarkers)
           drawMarker(i, starty, ypos);
@@ -190,6 +201,7 @@ public class IdCanvas extends JPanel
         }
 
         gg = (Graphics2D) image.getGraphics();
+
         //Fill in the background
         gg.setColor(Color.white);
         gg.fillRect(0, 0, getWidth(), imgHeight);
@@ -211,6 +223,7 @@ public class IdCanvas extends JPanel
                              av.getFont().getSize());
 
       gg.setFont(italic);
+      fm = gg.getFontMetrics();
 
       if (av.antiAlias)
         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
@@ -228,13 +241,16 @@ public class IdCanvas extends JPanel
             maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
 
           int annotationHeight = 0;
-          AnnotationLabels labels = null;
+
 
           if(av.showAnnotation)
           {
-            AnnotationPanel ap = new AnnotationPanel(av);
+            if (ap == null)
+              ap = new AnnotationPanel(av);
+
             annotationHeight = ap.adjustPanelHeight();
-            labels = new AnnotationLabels(av);
+            if (labels == null)
+              labels = new AnnotationLabels(av);
           }
 
           int hgap = av.charHeight;
@@ -279,10 +295,18 @@ public class IdCanvas extends JPanel
         else
         {
           //Now draw the id strings
+          int panelWidth = getWidth();
+          int xPos = 0;
 
+            SequenceI sequence;
             //Now draw the id strings
             for (int i = starty; i < endy; i++)
             {
+              sequence = av.alignment.getSequenceAt(i);
+
+              if(sequence==null)
+                continue;
+
               if (av.hasHiddenRows)
               {
                 setHiddenFont(i);
@@ -290,21 +314,21 @@ public class IdCanvas extends JPanel
 
                 // Selected sequence colours
                 if ( (searchResults != null) &&
-                    searchResults.contains(av.alignment.getSequenceAt(i)))
+                    searchResults.contains(sequence))
                 {
                   currentColor = Color.black;
                   currentTextColor = Color.white;
                 }
                 else if ( (av.getSelectionGroup() != null) &&
                          av.getSelectionGroup().getSequences(false).contains(
-                             av.alignment.getSequenceAt(i)))
+                             sequence))
                 {
                   currentColor = Color.lightGray;
                   currentTextColor = Color.black;
                 }
                 else
                 {
-                  currentColor = av.alignment.getSequenceAt(i).getColor();
+                  currentColor = av.getSequenceColour(sequence);
                   currentTextColor = Color.black;
                 }
 
@@ -315,9 +339,15 @@ public class IdCanvas extends JPanel
 
                 gg.setColor(currentTextColor);
 
-                String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());
+                String string = sequence.getDisplayId( av.getShowJVSuffix());
+
+
+                if(av.rightAlignIds)
+                {
+                  xPos = panelWidth - fm.stringWidth(string) - 4;
+                }
 
-                gg.drawString(string, 0,
+                gg.drawString(string, xPos,
                     (((i - starty) * av.charHeight) + av.charHeight) -
                     (av.charHeight / 5));
 
@@ -331,12 +361,32 @@ public class IdCanvas extends JPanel
 
     void drawMarker(int i, int starty, int yoffset)
     {
-      int hiddenIndex = av.adjustForHiddenSeqs(i);
-      int lastIndex = av.adjustForHiddenSeqs(i - 1);
-      int nextIndex = av.adjustForHiddenSeqs(i + 1);
+
+      SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+      //Use this method here instead of calling hiddenSeq adjust
+      //3 times.
+      int hSize = hseqs.length;
+
+      int hiddenIndex = i;
+      int lastIndex = i - 1;
+      int nextIndex = i + 1;
+
+      for(int j=0; j<hSize; j++)
+      {
+        if (hseqs[j] != null)
+        {
+          if(j-1<hiddenIndex)
+            hiddenIndex++;
+          if(j-1<lastIndex)
+            lastIndex++;
+          if(j-1<nextIndex)
+            nextIndex++;
+        }
+      }
 
       boolean below = (hiddenIndex > lastIndex + 1);
-      boolean above = (nextIndex>hiddenIndex+1);
+      boolean above = (nextIndex > hiddenIndex+1);
+
 
         gg.setColor(Color.blue);
         if(below)
@@ -375,7 +425,9 @@ public class IdCanvas extends JPanel
       Font bold = new Font(av.getFont().getName(), Font.BOLD,
                            av.getFont().getSize());
 
-      if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
+
+      if (av.alignment.getSequenceAt(i)!=null
+          && av.alignment.getSequenceAt(i).getHiddenSequences() != null)
         gg.setFont(bold);
       else
         gg.setFont(italic);