JAL-244 Allow adjusting Id column width in wrap mode. Set Id column width in gui...

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 838b381..e1c88e1 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -166,13 +166,9 @@ public class Commands
     if (avm == null)
       return true;
 
-    /*
-     * // script to execute after all loading is completed one way or another String
-     * groovyscript = m.get(Arg.GROOVY) == null ? null :
-     * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
-     * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
-     * DataSourceType protocol = null;
-     */
+    // set wrap scope here so it can be applied after structures are opened
+    boolean wrap = false;
+
     if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
     {
       commandArgsProvided = true;
@@ -256,11 +252,6 @@ public class Commands
           af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
                   format);
 
-          // wrap alignment?
-          boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
-                  null, "WRAP_ALIGNMENT", false);
-          af.getCurrentView().setWrapAlignment(wrap);
-
           // colour alignment?
           String colour = ArgParser.getFromSubValArgOrPref(avm, av,
                   Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
@@ -365,6 +356,12 @@ public class Commands
                     false, false);
           }
 
+          // wrap alignment? do this last for formatting reasons
+          wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, null,
+                  "WRAP_ALIGNMENT", false);
+          // af.setWrapFormat(wrap) is applied after structures are opened for
+          // annotation reasons
+
           // store the AlignFrame for this id
           afMap.put(id, af);
 
@@ -689,6 +686,15 @@ public class Commands
       }
     }
 
+    if (wrap)
+    {
+      AlignFrame af = afMap.get(id);
+      if (af != null)
+      {
+        af.setWrapFormat(wrap);
+      }
+    }
+
     /*
     boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
     if (doShading)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ab705c2..7f9bfff 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -157,7 +157,6 @@ import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
-import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -1456,9 +1455,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
-    try {
+    try
+    {
       htmlSVG.exportHTML(null);
-    } catch (ImageOutputException x) {
+    } catch (ImageOutputException x)
+    {
       // report problem to console and raise dialog
     }
   }
@@ -1467,51 +1468,64 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
-    try {
-    bjs.exportHTML(null);
-  } catch (ImageOutputException x) {
-    // report problem to console and raise dialog
-  }
+    try
+    {
+      bjs.exportHTML(null);
+    } catch (ImageOutputException x)
+    {
+      // report problem to console and raise dialog
+    }
   }
 
   public void createImageMap(File file, String image)
   {
-    try {
-    alignPanel.makePNGImageMap(file, image);
-    } catch (ImageOutputException x) {
+    try
+    {
+      alignPanel.makePNGImageMap(file, image);
+    } catch (ImageOutputException x)
+    {
       // report problem to console and raise dialog
     }
   }
 
   @Override
-  public void createPNG_actionPerformed(ActionEvent e) {
-    try{
+  public void createPNG_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       createPNG(null);
     } catch (ImageOutputException ioex)
     {
       // raise dialog, and report via console
     }
   }
+
   @Override
-  public void createEPS_actionPerformed(ActionEvent e) {
-    try{
+  public void createEPS_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       createEPS(null);
     } catch (ImageOutputException ioex)
     {
       // raise dialog, and report via console
     }
-    
+
   }
+
   @Override
-  public void createSVG_actionPerformed(ActionEvent e) {
-    try{
+  public void createSVG_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       createSVG(null);
     } catch (ImageOutputException ioex)
     {
       // raise dialog, and report via console
     }
-    
+
   }
+
   /**
    * Creates a PNG image of the alignment and writes it to the given file. If
    * the file is null, the user is prompted to choose a file.
@@ -1523,7 +1537,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
   }
 
-  public void createPNG(File f, String renderer, BitmapImageSizing userBis) throws ImageOutputException
+  public void createPNG(File f, String renderer, BitmapImageSizing userBis)
+          throws ImageOutputException
   {
     alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
   }
@@ -1534,7 +1549,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  public void createEPS(File f)  throws ImageOutputException
+  public void createEPS(File f) throws ImageOutputException
   {
     createEPS(f, null);
   }
@@ -1550,7 +1565,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
-  public void createSVG(File f)  throws ImageOutputException
+  public void createSVG(File f) throws ImageOutputException
   {
     createSVG(f, null);
   }
@@ -2341,12 +2356,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // annotation was duplicated earlier
             alignment.addAnnotation(sequences[i].getAnnotation()[a]);
             // take care of contact matrix too
-            ContactMatrixI cm=sequences[i].getContactMatrixFor(sequences[i].getAnnotation()[a]);
-            if (cm!=null)
+            ContactMatrixI cm = sequences[i]
+                    .getContactMatrixFor(sequences[i].getAnnotation()[a]);
+            if (cm != null)
             {
-              alignment.addContactListFor(sequences[i].getAnnotation()[a], cm);
+              alignment.addContactListFor(sequences[i].getAnnotation()[a],
+                      cm);
             }
-            
+
             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
                     a);
           }
@@ -3138,10 +3155,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-    scaleAbove.setVisible(wrapMenuItem.isSelected());
-    scaleLeft.setVisible(wrapMenuItem.isSelected());
-    scaleRight.setVisible(wrapMenuItem.isSelected());
-    viewport.setWrapAlignment(wrapMenuItem.isSelected());
+    setWrapFormat(wrapMenuItem.isSelected());
+  }
+
+  public void setWrapFormat(boolean b)
+  {
+    scaleAbove.setVisible(b);
+    scaleLeft.setVisible(b);
+    scaleRight.setVisible(b);
+    viewport.setWrapAlignment(b);
     alignPanel.updateLayout();
   }
 
@@ -4239,8 +4261,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return tp;
   }
 
-  public void showContactMapTree(AlignmentAnnotation aa,
-          ContactMatrixI cm)
+  public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm)
   {
     int x = 4, y = 5;
     int w = 400, h = 500;

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 8a43a4a..c7c03b3 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -297,7 +297,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
     int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
     int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
-    return calculateIdWidth(-1, false, true);
+    return calculateIdWidth(-1, false, false);
   }
 
   /**
@@ -624,7 +624,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     ranges.setStartSeq(0);
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
-    idwidthAdjuster.setVisible(!wrap);
+    // Allow idPanel width adjustment in wrap mode
+    idwidthAdjuster.setVisible(true);
 
     if (wrap)
     {
@@ -658,7 +659,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
     }
 
-    idSpaceFillerPanel1.setVisible(!wrap);
+    // idSpaceFillerPanel1.setVisible(!wrap);
 
     repaint();
   }
@@ -1437,8 +1438,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
 
-    if (System.getProperty("java.awt.headless") != null
-            && System.getProperty("java.awt.headless").equals("true"))
+    if (Jalview.isHeadlessMode())
     {
       seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
               - vscroll.getPreferredSize().width

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index afee3d0..241e0a3 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1206,6 +1206,7 @@ public class AnnotationLabels extends JPanel
         Graphics dummy = g2d.create();
         int newAnnotationIdWidth = drawLabels(dummy, clip, width, false,
                 null);
+        dummy.dispose();
         Dimension d = ap.calculateDefaultAlignmentIdWidth();
         int alignmentIdWidth = d.width;
         if (iwa != null && !iwa.manuallyAdjusted())
@@ -1230,6 +1231,14 @@ public class AnnotationLabels extends JPanel
         }
       }
     }
+    else
+    {
+      Graphics2D g2d = (Graphics2D) g;
+      Graphics dummy = g2d.create();
+      int newAnnotationIdWidth = drawLabels(dummy, clip, width, false,
+              null);
+      width = Math.max(newAnnotationIdWidth, givenWidth);
+    }
     drawLabels(g, clip, width, true, null);
   }
 
@@ -1255,7 +1264,7 @@ public class AnnotationLabels extends JPanel
           boolean actuallyDraw, FontMetrics fmetrics)
   {
     int actualWidth = 0;
-    if (actuallyDraw && g != null)
+    if (g != null)
     {
       if (av.getFont().getSize() < 10)
       {

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index c94dee0..d9997a0 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
+import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
@@ -382,6 +383,12 @@ public class IdCanvas extends JPanel implements ViewportListenerI
   void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
           int startSeq, int pageHeight)
   {
+    drawIdsWrapped(g, alignViewport, startSeq, pageHeight, -1);
+  }
+
+  void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
+          int startSeq, int pageHeight, int idWidth)
+  {
     int alignmentWidth = alignViewport.getAlignment().getWidth();
     final int alheight = alignViewport.getAlignment().getHeight();
 
@@ -429,7 +436,16 @@ public class IdCanvas extends JPanel implements ViewportListenerI
       if (labels != null && alignViewport.isShowAnnotation())
       {
         g.translate(0, ypos + (alheight * charHeight));
-        labels.drawComponent(g, getWidth());
+        int getAnnotationsIdWidth = labels.drawLabels(g, false, -1, false,
+                null);
+        int thisIdWidth = idWidth < 0 ? getAnnotationsIdWidth : idWidth;
+        if (thisIdWidth > getWidth())
+        {
+          this.setPreferredSize(
+                  new Dimension(this.getHeight(), thisIdWidth));
+          this.repaint();
+        }
+        labels.drawComponent(g, false, thisIdWidth);
         g.translate(0, -ypos - (alheight * charHeight));
       }