X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;fp=src%2Fjalview%2Fgui%2FSeqPanel.java;h=111b4c0112b6fec9a47ad37b7a90535fbb99f171;hb=afbff636fa2dfa01daa1f4ec4e8a936e61e3cf16;hp=454a73051a77a8330cb266217aae401a950931b7;hpb=c6df3928336440918d23b4e7cb579f134e2f48dd;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 454a730..111b4c0 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -44,7 +44,7 @@ import javax.swing.Timer;
 import javax.swing.ToolTipManager;
 
 import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
@@ -246,8 +246,7 @@ public class SeqPanel extends JPanel
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
-    
-    
+
     this.av = viewport;
     setBackground(Color.white);
 
@@ -342,6 +341,7 @@ public class SeqPanel extends JPanel
 
     return new MousePos(col, seqIndex, annIndex);
   }
+
   /**
    * Returns the aligned sequence position (base 0) at the mouse position, or
    * the closest visible one
@@ -483,8 +483,9 @@ public class SeqPanel extends JPanel
 
   void moveCursor(int dx, int dy)
   {
-    moveCursor(dx, dy,false);
+    moveCursor(dx, dy, false);
   }
+
   void moveCursor(int dx, int dy, boolean nextWord)
   {
     HiddenColumns hidden = av.getAlignment().getHiddenColumns();
@@ -492,11 +493,13 @@ public class SeqPanel extends JPanel
     if (nextWord)
     {
       int maxWidth = av.getAlignment().getWidth();
-      int maxHeight=av.getAlignment().getHeight();
-      SequenceI seqAtRow = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+      int maxHeight = av.getAlignment().getHeight();
+      SequenceI seqAtRow = av.getAlignment()
+              .getSequenceAt(seqCanvas.cursorY);
       // look for next gap or residue
-      boolean isGap = Comparison.isGap(seqAtRow.getCharAt(seqCanvas.cursorX));
-      int p = seqCanvas.cursorX,lastP,r=seqCanvas.cursorY,lastR;
+      boolean isGap = Comparison
+              .isGap(seqAtRow.getCharAt(seqCanvas.cursorX));
+      int p = seqCanvas.cursorX, lastP, r = seqCanvas.cursorY, lastR;
       do
       {
         lastP = p;
@@ -517,19 +520,23 @@ public class SeqPanel extends JPanel
         p = nextVisible(hidden, maxWidth, p, dx);
       } while ((dx != 0 ? p != lastP : r != lastR)
               && isGap == Comparison.isGap(seqAtRow.getCharAt(p)));
-      seqCanvas.cursorX=p;
-      seqCanvas.cursorY=r;
-    } else {
+      seqCanvas.cursorX = p;
+      seqCanvas.cursorY = r;
+    }
+    else
+    {
       int maxWidth = av.getAlignment().getWidth();
-      seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, dx);
+      seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX,
+              dx);
       seqCanvas.cursorY += dy;
     }
     scrollToVisible(false);
   }
 
-  private int nextVisible(HiddenColumns hidden,int maxWidth, int original, int dx)
+  private int nextVisible(HiddenColumns hidden, int maxWidth, int original,
+          int dx)
   {
-    int newCursorX=original+dx;
+    int newCursorX = original + dx;
     if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX))
     {
       int visx = hidden.absoluteToVisibleColumn(newCursorX - dx);
@@ -550,13 +557,13 @@ public class SeqPanel extends JPanel
       }
     }
     newCursorX = (newCursorX < 0) ? 0 : newCursorX;
-    if (newCursorX >= maxWidth
-            || !hidden.isVisible(newCursorX))
+    if (newCursorX >= maxWidth || !hidden.isVisible(newCursorX))
     {
       newCursorX = original;
     }
     return newCursorX;
   }
+
   /**
    * Scroll to make the cursor visible in the viewport.
    * 
@@ -612,7 +619,7 @@ public class SeqPanel extends JPanel
     if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
     {
       setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
-            seqCanvas.cursorX, seqCanvas.cursorY);
+              seqCanvas.cursorX, seqCanvas.cursorY);
     }
 
     if (repaintNeeded)
@@ -621,7 +628,6 @@ public class SeqPanel extends JPanel
     }
   }
 
-
   void setSelectionAreaAtCursor(boolean topLeft)
   {
     SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
@@ -960,8 +966,7 @@ public class SeqPanel extends JPanel
         SequenceI seq = match.getSequence();
         SequenceI ds = seq.getDatasetSequence() == null ? seq
                 : seq.getDatasetSequence();
-        MappedFeatures mf = fr2
-                .findComplementFeaturesAtResidue(ds, pos);
+        MappedFeatures mf = fr2.findComplementFeaturesAtResidue(ds, pos);
         if (mf != null)
         {
           for (SequenceFeature sf : mf.features)
@@ -1104,9 +1109,8 @@ public class SeqPanel extends JPanel
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtColumn(sequence, column + 1);
-      unshownFeatures = seqARep.appendFeatures(tooltipText, pos,
-              features, this.ap.getSeqPanel().seqCanvas.fr,
-              MAX_TOOLTIP_LENGTH);
+      unshownFeatures = seqARep.appendFeatures(tooltipText, pos, features,
+              this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH);
 
       /*
        * add features in CDS/protein complement at the corresponding
@@ -1124,8 +1128,8 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            unshownFeatures += seqARep.appendFeatures(tooltipText,
-                    pos, mf, fr2, MAX_TOOLTIP_LENGTH);
+            unshownFeatures += seqARep.appendFeatures(tooltipText, pos, mf,
+                    fr2, MAX_TOOLTIP_LENGTH);
           }
         }
       }
@@ -1153,8 +1157,7 @@ public class SeqPanel extends JPanel
       if (!textString.equals(lastTooltip))
       {
         lastTooltip = textString;
-        lastFormattedTooltip = JvSwingUtils.wrapTooltip(true,
-                textString);
+        lastFormattedTooltip = JvSwingUtils.wrapTooltip(true, textString);
         setToolTipText(lastFormattedTooltip);
       }
     }
@@ -1181,7 +1184,8 @@ public class SeqPanel extends JPanel
 
     String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column,
             anns);
-    if (!tooltip.equals(lastTooltip))
+    if (tooltip == null ? tooltip != lastTooltip
+            : !tooltip.equals(lastTooltip))
     {
       lastTooltip = tooltip;
       lastFormattedTooltip = tooltip == null ? null
@@ -1237,8 +1241,8 @@ public class SeqPanel extends JPanel
 
     tempTip.setTipText(lastFormattedTooltip);
     int tipWidth = (int) tempTip.getPreferredSize().getWidth();
-    
-    // was      x += (w - x < 200) ? -(w / 2) : 5;
+
+    // was x += (w - x < 200) ? -(w / 2) : 5;
     x = (x + tipWidth < w ? x + 10 : w - tipWidth);
     Point p = new Point(x, y + av.getCharHeight()); // BH 2018 was - 20?
 
@@ -1252,7 +1256,8 @@ public class SeqPanel extends JPanel
    * changed, so selective redraws can be applied (ie. only structures, only
    * overview, etc)
    */
-  private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
+  private boolean updateOverviewAndStructs = false; // TODO: refactor to
+                                                    // avcontroller
 
   /**
    * set if av.getSelectionGroup() refers to a group that is defined on the
@@ -1314,8 +1319,7 @@ public class SeqPanel extends JPanel
      * Sequence number (if known), and sequence name.
      */
     String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
-    text.append("Sequence").append(seqno).append(" ID: ")
-            .append(seqName);
+    text.append("Sequence").append(seqno).append(" ID: ").append(seqName);
 
     String residue = null;
 
@@ -1574,12 +1578,12 @@ public class SeqPanel extends JPanel
     String label = null;
     if (groupEditing)
     {
-        message.append("Edit group:");
+      message.append("Edit group:");
       label = MessageManager.getString("action.edit_group");
     }
     else
     {
-        message.append("Edit sequence: " + seq.getName());
+      message.append("Edit sequence: " + seq.getName());
       label = seq.getName();
       if (label.length() > 10)
       {
@@ -1771,8 +1775,7 @@ public class SeqPanel extends JPanel
           {
             for (int j = 0; j < startres - editLastRes; j++)
             {
-              if (!Comparison
-                      .isGap(groupSeqs[g].getCharAt(fixedRight - j)))
+              if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
               {
                 blank = false;
                 break;
@@ -2164,8 +2167,8 @@ public class SeqPanel extends JPanel
          * highlight the first feature at the position on the alignment
          */
         SearchResultsI highlight = new SearchResults();
-        highlight.addResult(sequence, features.get(0).getBegin(), features
-                .get(0).getEnd());
+        highlight.addResult(sequence, features.get(0).getBegin(),
+                features.get(0).getEnd());
         seqCanvas.highlightSearchResults(highlight, true);
 
         /*
@@ -2429,7 +2432,7 @@ public class SeqPanel extends JPanel
       return;
     }
 
-    res = Math.min(res, av.getAlignment().getWidth()-1);
+    res = Math.min(res, av.getAlignment().getWidth() - 1);
 
     if (stretchGroup.getEndRes() == res)
     {
@@ -2802,7 +2805,7 @@ public class SeqPanel extends JPanel
     {
       if (av.getAlignment() == null)
       {
-        Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+        Console.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
                 + " ViewId=" + av.getViewId()
                 + " 's alignment is NULL! returning immediately.");
         return;