X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=190682941a129aca2ff76b5377fa7860c4c803a1;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=e29a0e2df84f47afb4b3e79f09f2d4caec54884f;hpb=e81459b192f4d635c1cd96befa7b14992d12ee5e;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index e29a0e2..1906829 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -76,6 +76,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   private IdPanel idPanel;
 
   private boolean headless;
+
   IdwidthAdjuster idwidthAdjuster;
 
   /** DOCUMENT ME!! */
@@ -155,6 +156,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     return av;
   }
+
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
@@ -177,8 +179,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
             + fm.getDescent()));
     idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
-            .getCharHeight()
-            + fm.getDescent()));
+            .getCharHeight() + fm.getDescent()));
 
     getIdPanel().getIdCanvas().gg = null;
     getSeqPanel().seqCanvas.img = null;
@@ -317,7 +318,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param redrawOverview
    * @return
    */
-  public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview)
+  public boolean scrollToPosition(SearchResults searchResults,
+          boolean redrawOverview)
   {
     return scrollToPosition(searchResults, 0, redrawOverview, false);
   }
@@ -337,8 +339,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @return false if results were not found
    */
   public boolean scrollToPosition(SearchResults results,
-          int verticalOffset,
-          boolean redrawOverview, boolean centre)
+          int verticalOffset, boolean redrawOverview, boolean centre)
   {
     int startv, endv, starts, ends;
     // TODO: properly locate search results in view when large numbers of hidden
@@ -363,8 +364,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       int start = r[0];
       int end = r[1];
       // DEBUG
-//       System.err.println(this.av.viewName + " Seq : " + seqIndex
-//       + " Scroll to " + start + "," + end);
+      // System.err.println(this.av.viewName + " Seq : " + seqIndex
+      // + " Scroll to " + start + "," + end);
 
       /*
        * To centre results, scroll to positions half the visible width
@@ -747,7 +748,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
+      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+              .getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
@@ -844,13 +846,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
-    sorter.sort(getAlignment()
-            .getAlignmentAnnotation(),
+    sorter.sort(getAlignment().getAlignmentAnnotation(),
             av.getSortAnnotationsBy());
     repaint();
 
     if (updateOverview)
     {
+      // TODO: determine if this paintAlignment changed structure colours
       av.getStructureSelectionManager().sequenceColoursChanged(this);
 
       if (overviewPanel != null)
@@ -1062,9 +1064,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 - 4;
       }
 
-      pg.drawString(
-              seq.getDisplayId(av.getShowJVSuffix()),
-              xPos,
+      pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
               (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
                       - (av.getCharHeight() / 5));
     }
@@ -1073,7 +1073,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     // draw main sequence panel
     pg.translate(idWidth, 0);
-    getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+    getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq,
+            endSeq, 0);
 
     if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
     {
@@ -1175,12 +1176,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       if (labels != null)
       {
-        pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.getCharHeight()));
+        pg.translate(-3,
+                ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
 
         pg.setFont(av.getFont());
         labels.drawComponent(pg, idWidth);
-        pg.translate(+3, -ypos
+        pg.translate(
+                +3,
+                -ypos
                         - (av.getAlignment().getHeight() * av
                                 .getCharHeight()));
       }
@@ -1190,8 +1193,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pg.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
-            0);
+    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+            totalHeight, 0);
 
     if ((pi * pheight) < totalHeight)
     {
@@ -1249,8 +1252,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (alignFrame != null && !headless)
     {
       alignFrame.setProgressBar(MessageManager.formatMessage(
-              "status.saving_file", new Object[]
-              { type.getLabel() }), progress);
+              "status.saving_file", new Object[] { type.getLabel() }),
+              progress);
     }
     try
     {
@@ -1311,7 +1314,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       if (alignFrame != null && !headless)
       {
-        alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
+        alignFrame.setProgressBar(
+                MessageManager.getString("status.export_complete"),
+                progress);
       }
     }
   }
@@ -1376,6 +1381,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
   }
+
   public void makePNGImageMap(File imgMapFile, String imageName)
   {
     // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
@@ -1413,8 +1419,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
             if (av.getAlignment().isNucleotide())
             {
               triplet = ResidueProperties.nucleotideName.get(seq
-                      .getCharAt(res)
-                      + "");
+                      .getCharAt(res) + "");
             }
             else
             {
@@ -1436,8 +1441,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 text.append("<area shape=\"rect\" coords=\""
                         + (idWidth + res * av.getCharWidth()) + "," + sy
                         + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + ","
-                        + (av.getCharHeight() + sy) + "\""
+                        + "," + (av.getCharHeight() + sy) + "\""
                         + " onMouseOver=\"toolTip('" + alIndex + " "
                         + triplet);
               }
@@ -1456,8 +1460,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 text.append("<area shape=\"rect\" coords=\""
                         + (idWidth + res * av.getCharWidth()) + "," + sy
                         + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + ","
-                        + (av.getCharHeight() + sy) + "\""
+                        + "," + (av.getCharHeight() + sy) + "\""
                         + " onMouseOver=\"toolTip('" + alIndex + " "
                         + triplet);
               }
@@ -1616,7 +1619,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return av == null ? null : av.getAlignment();
   }
 
-
   @Override
   public String getViewName()
   {
@@ -1668,12 +1670,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     return new FeatureRenderer(this);
   }
-  @Override 
+
+  @Override
   public jalview.api.FeatureRenderer getFeatureRenderer()
   {
     return seqPanel.seqCanvas.getFeatureRenderer();
   }
-  public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
+
+  public void updateFeatureRenderer(
+          jalview.renderer.seqfeatures.FeatureRenderer fr)
   {
     fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
   }