X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=e84aae0758c77af11c5c011c42b814b71fbe18ee;hb=53f3ef526cdbea018a1cda6742d28e03cca4ed20;hp=065872fbd43182094b94b2526804c33f0d0ef9a4;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 065872f..e84aae0 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -24,6 +24,7 @@ import jalview.analysis.AnnotationSorter;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
@@ -122,7 +123,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
-//	setBackground(Color.white);  // BH 2019
+    // setBackground(Color.white); // BH 2019
     alignFrame = af;
     this.av = av;
     setSeqPanel(new SeqPanel(av, this));
@@ -471,8 +472,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         /*
          * Scroll down to make end of search results visible
          */
-        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
-                + 1);
+        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
       }
       /*
        * Else results are already visible - no need to scroll
@@ -572,7 +572,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Dimension e = idPanel.getSize();
     alabels.setSize(new Dimension(e.width, annotationHeight));
 
-
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), annotationHeight));
     annotationScroller.validate();
@@ -806,7 +805,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // could not be validated and it is not clear if it is now being
           // called. Log warning here in case it is called and unforeseen
           // problems occur
-          Cache.warn(
+          Console.warn(
                   "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
 
           // scroll to start of panel
@@ -1020,8 +1019,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * single graphics context), then reset to (0, scale height)
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
-    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
-            endRes, startSeq, endSeq - 1);
+    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics,
+            startRes, endRes, startSeq, endSeq - 1);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
     if (av.isShowAnnotation() && (endSeq == alignmentHeight))
@@ -1065,8 +1064,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @throws PrinterException
    */
-  public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
-          Graphics g) throws PrinterException
+  public int printWrappedAlignment(int pageWidth, int pageHeight,
+          int pageNumber, Graphics g) throws PrinterException
   {
     getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(),
             getHeight());
@@ -1118,8 +1117,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     g.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
-            totalHeight, 0);
+    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g,
+            pageWidth - idWidth, totalHeight, 0);
 
     if ((pageNumber * pageHeight) < totalHeight)
     {
@@ -1284,13 +1283,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
-              triplet = ResidueProperties.nucleotideName.get(seq
-                      .getCharAt(column) + "");
+              triplet = ResidueProperties.nucleotideName
+                      .get(seq.getCharAt(column) + "");
             }
             else
             {
-              triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
-                      + "");
+              triplet = ResidueProperties.aa2Triplet
+                      .get(seq.getCharAt(column) + "");
             }
 
             if (triplet == null)
@@ -1307,7 +1306,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 text.append("<area shape=\"rect\" coords=\"")
                         .append((idWidth + column * av.getCharWidth()))
                         .append(",").append(sy).append(",")
-                        .append((idWidth + (column + 1) * av.getCharWidth()))
+                        .append((idWidth
+                                + (column + 1) * av.getCharWidth()))
                         .append(",").append((av.getCharHeight() + sy))
                         .append("\"").append(" onMouseOver=\"toolTip('")
                         .append(seqPos).append(" ").append(triplet);
@@ -1333,7 +1333,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
             }
             if (!Comparison.isGap(seq.getCharAt(column)))
             {
-              List<SequenceFeature> features = seq.findFeatures(column, column);
+              List<SequenceFeature> features = seq.findFeatures(column,
+                      column);
               for (SequenceFeature sf : features)
               {
                 if (sf.isContactFeature())
@@ -1464,9 +1465,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      if (Cache.isDebugEnabled())
+      if (Console.isDebugEnabled())
       {
-        Cache.warn("Closing alignment panel which is already closed.");
+        Console.warn("Closing alignment panel which is already closed.");
       }
     }
   }
@@ -1546,11 +1547,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
       setAlignFrameView();
     }
   }
+
   public void setAlignFrameView()
   {
     alignFrame.setDisplayedView(this);
   }
-  
+
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {