git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
Set wrapped mode even if false
[jalview.git] / src / jalview / gui / SeqCanvas.java
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index d9f7ebb..8623872 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -133,9 +133,16 @@ public class SeqCanvas extends JComponent
         ypos += av.charHeight;\r
 \r
         if(av.hasHiddenColumns)\r
-                startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+        {\r
+          startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+          endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+        }\r
 \r
-        // EAST SCALE\r
+        int maxwidth = av.alignment.getWidth();\r
+        if (av.hasHiddenColumns)\r
+            maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
+        // WEST SCALE\r
         for (int i = 0; i < av.alignment.getHeight(); i++)\r
         {\r
             SequenceI seq = av.alignment.getSequenceAt(i);\r
@@ -404,19 +411,16 @@ public class SeqCanvas extends JComponent
     public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
         int startRes)\r
     {\r
-\r
         AlignmentI al = av.getAlignment();\r
 \r
         FontMetrics fm = getFontMetrics(av.getFont());\r
 \r
-        int LABEL_EAST = 0;\r
 \r
         if (av.scaleRightWrapped)\r
         {\r
             LABEL_EAST = fm.stringWidth(getMask());\r
         }\r
 \r
-        int LABEL_WEST = 0;\r
 \r
         if (av.scaleLeftWrapped)\r
         {\r
@@ -437,14 +441,18 @@ public class SeqCanvas extends JComponent
 \r
         int endx;\r
         int ypos = hgap;\r
+        int maxwidth = av.alignment.getWidth();\r
+\r
+        if(av.hasHiddenColumns)\r
+          maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;\r
 \r
-        while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
+        while ((ypos <= canvasHeight) && (startRes < maxwidth))\r
         {\r
           endx = startRes + cWidth -1;\r
 \r
-          if (endx > al.getWidth())\r
+          if (endx > maxwidth)\r
           {\r
-            endx = al.getWidth();\r
+            endx = maxwidth;\r
           }\r
 \r
             g.setFont(av.getFont());\r
@@ -469,6 +477,35 @@ public class SeqCanvas extends JComponent
                 drawNorthScale(g, startRes, endx, ypos);\r
             }\r
 \r
+            if (av.hasHiddenColumns && av.showHiddenMarkers)\r
+            {\r
+              g.setColor(Color.blue);\r
+              int res;\r
+              for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();\r
+                   i++)\r
+              {\r
+                res = av.getColumnSelection().findHiddenRegionPosition(i) -\r
+                    startRes;\r
+\r
+                if (res < 0 || res > endx - startRes)\r
+                  continue;\r
+\r
+                gg.fillPolygon(new int[]\r
+                               {res * av.charWidth - av.charHeight / 4,\r
+                               res * av.charWidth + av.charHeight / 4,\r
+                               res * av.charWidth},\r
+                               new int[]\r
+                               {\r
+                               ypos - (av.charHeight / 2),\r
+                               ypos - (av.charHeight / 2),\r
+                               ypos - (av.charHeight / 2) + 8\r
+                }, 3);\r
+\r
+              }\r
+            }\r
+\r
+\r
+\r
             // When printing we have an extra clipped region,\r
             // the Printable page which we need to account for here\r
             Shape clip = g.getClip();\r
@@ -560,15 +597,14 @@ public class SeqCanvas extends JComponent
 \r
           draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
 \r
-          g1.setColor(Color.blue);\r
-          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,\r
-                      startSeq + offset,\r
-                      (blockEnd - blockStart + 1) * av.charWidth - 1,\r
-                      startSeq + (endSeq - startSeq) * av.charHeight + offset);\r
-          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth,\r
-                      startSeq + offset,\r
-                      (blockEnd - blockStart + 1) * av.charWidth,\r
-                      startSeq + (endSeq - startSeq) * av.charHeight + offset);\r
+          if(av.getShowHiddenMarkers())\r
+          {\r
+            g1.setColor(Color.blue);\r
+            g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,\r
+                        startSeq + offset,\r
+                        (blockEnd - blockStart + 1) * av.charWidth - 1,\r
+                        startSeq + (endSeq - startSeq) * av.charHeight + offset);\r
+          }\r
 \r
           g1.translate( -screenY * av.charWidth, 0);\r
           screenY += blockEnd - blockStart + 1;\r
@@ -580,6 +616,7 @@ public class SeqCanvas extends JComponent
           blockEnd = blockStart + (endRes - startRes) - screenY;\r
           g1.translate(screenY * av.charWidth, 0);\r
           draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
           g1.translate( -screenY * av.charWidth, 0);\r
         }\r
       }\r
@@ -591,14 +628,11 @@ public class SeqCanvas extends JComponent
 \r
     //int startRes, int endRes, int startSeq, int endSeq, int x, int y,\r
     // int x1, int x2, int y1, int y2, int startx, int starty,\r
-    void draw(Graphics g1,\r
+    void draw(Graphics g,\r
                    int startRes, int endRes,\r
                    int startSeq, int endSeq,\r
                    int offset)\r
    {\r
-\r
-\r
-      Graphics2D g = (Graphics2D) g1;\r
       g.setFont(av.getFont());\r
       sr.prepare(g, av.renderGaps);\r
 \r
@@ -616,7 +650,7 @@ public class SeqCanvas extends JComponent
 \r
             if (av.showSequenceFeatures)\r
             {\r
-                fr.drawSequence(g1, nextSeq, startRes, endRes,\r
+                fr.drawSequence(g, nextSeq, startRes, endRes,\r
                     offset + ((i - startSeq) * av.charHeight));\r
             }\r
 \r
@@ -643,6 +677,17 @@ public class SeqCanvas extends JComponent
             }\r
           }\r
 \r
+          if(av.getSelectionGroup()!=null || av.alignment.getGroups().size()>0)\r
+            drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);\r
+\r
+   }\r
+\r
+   void drawGroupsBoundaries(Graphics g1,\r
+                   int startRes, int endRes,\r
+                   int startSeq, int endSeq,\r
+                   int offset)\r
+   {\r
+       Graphics2D g = (Graphics2D)g1;\r
         //\r
         /////////////////////////////////////\r
         // Now outline any areas if necessary\r
@@ -683,11 +728,11 @@ public class SeqCanvas extends JComponent
                     }\r
 \r
                     if ( (sx <= (endRes-startRes)*av.charWidth) &&\r
-                            group.sequences.contains(av.alignment.getSequenceAt(\r
-                                    i)))\r
+                            group.getSequences(false).\r
+                            contains(av.alignment.getSequenceAt(i)))\r
                     {\r
                         if ((bottom == -1) &&\r
-                                !group.sequences.contains(\r
+                                !group.getSequences(false).contains(\r
                                     av.alignment.getSequenceAt(i + 1)))\r
                         {\r
                             bottom = sy + av.charHeight;\r
@@ -696,7 +741,7 @@ public class SeqCanvas extends JComponent
                         if (!inGroup)\r
                         {\r
                             if (((top == -1) && (i == 0)) ||\r
-                                    !group.sequences.contains(\r
+                                    !group.getSequences(false).contains(\r
                                         av.alignment.getSequenceAt(i - 1)))\r
                             {\r
                                 top = sy;\r
@@ -802,9 +847,13 @@ public class SeqCanvas extends JComponent
                 }\r
 \r
                 group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
+\r
+                g.setStroke(new BasicStroke());\r
             }\r
             while (groupIndex < av.alignment.getGroups().size());\r
+\r
         }\r
+\r
     }\r
 \r
     /**\r