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ignore begin==0 and end==0 for the moment
authoramwaterhouse <Andrew Waterhouse>
Wed, 7 Jun 2006 12:58:21 +0000 (12:58 +0000)
committeramwaterhouse <Andrew Waterhouse>
Wed, 7 Jun 2006 12:58:21 +0000 (12:58 +0000)
src/jalview/gui/FeatureSettings.java patch | blob | history
src/jalview/gui/SeqPanel.java patch | blob | history

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 5565292..7917efa 100755 (executable)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -169,9 +169,16 @@ public class FeatureSettings extends JPanel
       alignmentHasFeatures = true;\r
 \r
       tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+\r
       int index = 0;\r
       while (index < tmpfeatures.length)\r
       {\r
+        if(tmpfeatures[index].begin == 0 && tmpfeatures[index].end ==0)\r
+        {\r
+          index++;\r
+          continue;\r
+        }\r
+\r
         if(tmpfeatures[index].getFeatureGroup()!=null)\r
         {\r
           group = tmpfeatures[index].featureGroup;\r
@@ -257,6 +264,12 @@ public class FeatureSettings extends JPanel
         {\r
           group = tmpfeatures[index].featureGroup;\r
 \r
+          if(tmpfeatures[index].begin==0 && tmpfeatures[index].end==0)\r
+          {\r
+            index ++;\r
+            continue;\r
+          }\r
+\r
           if (group==null || fr.featureGroups.get(group)==null ||\r
               ((Boolean) fr.featureGroups.get(group)).booleanValue())\r
           {\r
@@ -300,6 +313,10 @@ public class FeatureSettings extends JPanel
       //which was just selected\r
       type = visibleChecks.elementAt(i).toString();\r
       data[dataIndex][0] = type;\r
+\r
+      if(fr.getColour(type)==null)\r
+        fr.createRandomColour(type);\r
+\r
       data[dataIndex][1] = fr.getColour(type);\r
       data[dataIndex][2] = new Boolean(true);\r
       dataIndex++;\r
@@ -429,8 +446,6 @@ public class FeatureSettings extends JPanel
             Enumeration e = fr.featureColours.keys();\r
            while(e.hasMoreElements())\r
            {\r
-\r
-\r
                 jalview.binding.Colour col = new jalview.binding.Colour();\r
                 col.setName(e.nextElement().toString());\r
                 col.setRGB(jalview.util.Format.getHexString(\r
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 126d755..19ee273 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -27,6 +27,8 @@ import java.awt.event.*;
 \r
 import javax.swing.*;\r
 \r
+import java.util.Vector;\r
+\r
 \r
 /**\r
  * DOCUMENT ME!\r
@@ -70,6 +72,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     StringBuffer keyboardNo1;\r
     StringBuffer keyboardNo2;\r
 \r
+    java.net.URL linkImageURL;\r
+\r
     /**\r
      * Creates a new SeqPanel object.\r
      *\r
@@ -78,6 +82,7 @@ public class SeqPanel extends JPanel implements MouseListener,
      */\r
     public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
     {\r
+        linkImageURL = getClass().getResource("/images/link.gif");\r
         ToolTipManager.sharedInstance().registerComponent(this);\r
         ToolTipManager.sharedInstance().setInitialDelay(0);\r
         ToolTipManager.sharedInstance().setDismissDelay(10000);\r
@@ -167,6 +172,29 @@ public class SeqPanel extends JPanel implements MouseListener,
      return seq;\r
    }\r
 \r
+   Vector getAllFeaturesAtRes(SequenceI seq, int res)\r
+   {\r
+     Vector allFeatures = new Vector();\r
+     int index = 0;\r
+     if(seq.getSequenceFeatures()!=null)\r
+     {\r
+       while (index < seq.getSequenceFeatures().length)\r
+       {\r
+         SequenceFeature sf = seq.getSequenceFeatures()[index];\r
+         if (sf.getBegin() <= res &&\r
+             sf.getEnd() >= res)\r
+         {\r
+           if (av.featuresDisplayed.containsKey(sf.getType()))\r
+           {\r
+             allFeatures.addElement(sf);\r
+           }\r
+         }\r
+         index++;\r
+       }\r
+     }\r
+     return allFeatures;\r
+  }\r
+\r
    void endEditing()\r
    {\r
      startseq = -1;\r
@@ -501,6 +529,7 @@ public class SeqPanel extends JPanel implements MouseListener,
             if(features!=null)\r
             {\r
               StringBuffer sbuffer = new StringBuffer("<html>");\r
+              StringBuffer seqSpecific =  new StringBuffer();\r
 \r
               for (int i = 0; i < features.length; i++)\r
               {\r
@@ -522,16 +551,19 @@ public class SeqPanel extends JPanel implements MouseListener,
                         sbuffer.append("<br>");\r
                       sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +\r
                                      features[i].getEnd());\r
+                      if (features[i].links != null)\r
+                      sbuffer.append("<img src=\"" + linkImageURL + "\">");\r
                     }\r
                   }\r
                   else\r
                   {\r
                     if (sbuffer.length() > 6)\r
                       sbuffer.append("<br>");\r
-                    if(features[i].featureGroup!=null)\r
-                      sbuffer.append(features[i].featureGroup+";");\r
 \r
-                    sbuffer.append(features[i].getType());\r
+                    sbuffer.append(features[i].getType() + " " +\r
+                                   features[i].begin);\r
+                    if (features[i].begin != features[i].end)\r
+                      sbuffer.append(" " + features[i].end);\r
 \r
                     if (features[i].getDescription() != null\r
                         && !features[i].description.equals(features[i].getType()))\r
@@ -541,11 +573,24 @@ public class SeqPanel extends JPanel implements MouseListener,
                     {\r
                       sbuffer.append("; (" + features[i].getStatus() + ")");\r
                     }\r
+                    if (features[i].links != null)\r
+                      sbuffer.append("<img src=\"" + linkImageURL + "\">");\r
+\r
                   }\r
                 }\r
+                else if(features[i].begin==0 && features[i].end==0)\r
+                {\r
+                  // seqSpecific.append(features[i].featureGroup+": "\r
+                  //                   + features[i].getType()+" "\r
+                   //                   +features[i].getDescription()+"<br>");\r
 \r
+                }\r
               }\r
 \r
+              if(seqSpecific.length()>0)\r
+                seqSpecific.setLength(seqSpecific.length()-4);\r
+\r
+              sbuffer.append(seqSpecific);\r
               sbuffer.append("</html>");\r
               if(sbuffer.length()==13) // <html></html>\r
                 setToolTipText("");\r
@@ -1145,7 +1190,7 @@ public class SeqPanel extends JPanel implements MouseListener,
               "Cannot edit annotations in wrapped view.",\r
               "Wrapped view - no edit",\r
               JOptionPane.WARNING_MESSAGE);\r
-        return;\r
+          return;\r
       }\r
 \r
       if(seq<0 || res<0)\r
@@ -1190,12 +1235,13 @@ public class SeqPanel extends JPanel implements MouseListener,
                             (allGroups[i].getEndRes() >= res))\r
                     {\r
                         stretchGroup = allGroups[i];\r
-                        av.setSelectionGroup(stretchGroup);\r
-\r
                         break;\r
                     }\r
                 }\r
             }\r
+\r
+            av.setSelectionGroup(stretchGroup);\r
+\r
         }\r
 \r
         if (av.cursorMode)\r
@@ -1207,49 +1253,65 @@ public class SeqPanel extends JPanel implements MouseListener,
         }\r
 \r
 \r
-        if (stretchGroup == null)\r
+        if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
         {\r
-            // define a new group here\r
-            SequenceGroup sg = new SequenceGroup();\r
-            sg.setStartRes(res);\r
-            sg.setEndRes(res);\r
-            sg.addSequence(sequence, false);\r
-            av.setSelectionGroup(sg);\r
-            stretchGroup = sg;\r
-\r
-            if (av.getConservationSelected())\r
+          Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),\r
+                                                  sequence.findPosition(res));\r
+          Vector links = new Vector();;\r
+            for (int i = 0; i < allFeatures.size(); i++)\r
             {\r
-                SliderPanel.setConservationSlider(ap,\r
-                    av.getGlobalColourScheme(), "Background");\r
+              SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);\r
+              if (sf.links != null)\r
+              {\r
+                for (int j = 0; j < sf.links.size(); j++)\r
+                {\r
+                  links.addElement(sf.links.elementAt(j));\r
+                }\r
+              }\r
             }\r
 \r
-            if (av.getAbovePIDThreshold())\r
-            {\r
-                SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
-                    "Background");\r
-            }\r
+\r
+          jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);\r
+          pop.show(this, evt.getX(), evt.getY());\r
         }\r
-        else if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
+        else if (stretchGroup == null)\r
         {\r
-            jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);\r
-            pop.show(this, evt.getX(), evt.getY());\r
+          //Only if left mouse button do we want to change group sizes\r
 \r
-            // edit the properties of existing group\r
-        }\r
+          // define a new group here\r
+          SequenceGroup sg = new SequenceGroup();\r
+          sg.setStartRes(res);\r
+          sg.setEndRes(res);\r
+          sg.addSequence(sequence, false);\r
+          av.setSelectionGroup(sg);\r
+          stretchGroup = sg;\r
 \r
-        if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))\r
-        {\r
+          if (av.getConservationSelected())\r
+          {\r
+            SliderPanel.setConservationSlider(ap,\r
+                                              av.getGlobalColourScheme(),\r
+                                              "Background");\r
+          }\r
+\r
+          if (av.getAbovePIDThreshold())\r
+          {\r
+            SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
+                                           "Background");\r
+          }\r
+          if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))\r
+          {\r
             // Edit end res position of selected group\r
             changeEndRes = true;\r
-        }\r
-        else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))\r
-        {\r
+          }\r
+          else if ( (stretchGroup != null) &&\r
+                   (stretchGroup.getStartRes() == res))\r
+          {\r
             // Edit end res position of selected group\r
             changeStartRes = true;\r
+          }\r
+          stretchGroup.getWidth();\r
         }\r
 \r
-        stretchGroup.getWidth();\r
-\r
         seqCanvas.repaint();\r
     }\r
 \r