Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 2396329..ce87c01 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);
   }
 
   /**
@@ -338,18 +338,27 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // Also check annotation label widths
     if (includeAnnotations && al.getAlignmentAnnotation() != null)
     {
-      fm = c.getFontMetrics(getAlabels().getFont());
-
-      for (i = 0; i < al.getAlignmentAnnotation().length; i++)
+      if (Jalview.isHeadlessMode())
+      {
+        AnnotationLabels aal = getAlabels();
+        int stringWidth = aal.drawLabels(null, false, idWidth, false, false, fm);
+        idWidth = Math.max(idWidth, stringWidth);
+      }
+      else
       {
-        AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
-        if (visibleOnly && !aa.visible)
+        fm = c.getFontMetrics(getAlabels().getFont());
+
+        for (i = 0; i < al.getAlignmentAnnotation().length; i++)
         {
-          continue;
+          AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
+          if (visibleOnly && !aa.visible)
+          {
+            continue;
+          }
+          String label = aa.label;
+          int stringWidth = fm.stringWidth(label);
+          idWidth = Math.max(idWidth, stringWidth);
         }
-        String label = aa.label;
-        int stringWidth = fm.stringWidth(label);
-        idWidth = Math.max(idWidth, stringWidth);
       }
     }
 
@@ -557,7 +566,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // this is called after loading new annotation onto alignment
     if (alignFrame.getHeight() == 0)
     {
-      System.out.println("NEEDS FIXING");
+      jalview.bin.Console.outPrintln("NEEDS FIXING");
     }
     validateAnnotationDimensions(true);
     addNotify();
@@ -581,21 +590,29 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // not be called directly by programs.
     // I note that addNotify() is called in several areas of Jalview.
 
-    int annotationHeight = getAnnotationPanel().adjustPanelHeight();
-    annotationHeight = getAnnotationPanel()
-            .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
+    AnnotationPanel ap = getAnnotationPanel();
+    int annotationHeight = ap.adjustPanelHeight();
+    annotationHeight = ap.adjustForAlignFrame(adjustPanelHeight,
+            annotationHeight);
 
     hscroll.addNotify();
-    annotationScroller.setPreferredSize(
-            new Dimension(annotationScroller.getWidth(), annotationHeight));
-
     Dimension e = idPanel.getSize();
-    alabels.setSize(new Dimension(e.width, annotationHeight));
+    int idWidth = e.width;
+    boolean manuallyAdjusted = this.getIdPanel().getIdCanvas()
+            .manuallyAdjusted();
+    annotationScroller.setPreferredSize(new Dimension(
+            manuallyAdjusted ? idWidth : annotationScroller.getWidth(),
+            annotationHeight));
+
+    alabels.setPreferredSize(new Dimension(idWidth, annotationHeight));
 
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-            annotationSpaceFillerHolder.getWidth(), annotationHeight));
+            manuallyAdjusted ? idWidth
+                    : annotationSpaceFillerHolder.getWidth(),
+            annotationHeight));
     annotationScroller.validate();
     annotationScroller.addNotify();
+    ap.validate();
   }
 
   /**
@@ -611,9 +628,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
     boolean wrap = av.getWrapAlignment();
     ViewportRanges ranges = av.getRanges();
     ranges.setStartSeq(0);
-    scalePanelHolder.setVisible(!wrap);
+    // scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
-    idwidthAdjuster.setVisible(!wrap);
+    // Allow idPanel width adjustment in wrap mode
+    idwidthAdjuster.setVisible(true);
 
     if (wrap)
     {
@@ -647,7 +665,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
     }
 
-    idSpaceFillerPanel1.setVisible(!wrap);
+    // idSpaceFillerPanel1.setVisible(!wrap);
 
     repaint();
   }
@@ -868,10 +886,27 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public void paintComponent(Graphics g)
   {
     invalidate(); // needed so that the id width adjuster works correctly
-
     Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
-    idPanelHolder.setPreferredSize(d);
-    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+    int idWidth = d.width;
+
+    // check wrapped alignment as at least 1 residue width
+    if (av.getWrapAlignment())
+    {
+      SeqCanvas sc = this.getSeqPanel().seqCanvas;
+      if (sc != null && sc.getWidth() < sc.getMinimumWrappedCanvasWidth())
+      {
+        // need to make some adjustments
+        idWidth -= (sc.getMinimumWrappedCanvasWidth() - sc.getWidth());
+        av.setIdWidth(idWidth);
+        av.getAlignPanel().getIdPanel().getIdCanvas()
+                .setManuallyAdjusted(true);
+
+        validateAnnotationDimensions(false);
+      }
+    }
+
+    idPanelHolder.setPreferredSize(new Dimension(idWidth, d.height));
+    hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12));
 
     validate(); // needed so that the id width adjuster works correctly
 
@@ -1029,7 +1064,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     List<SequenceI> selection = av.getSelectionGroup() == null ? null
             : av.getSelectionGroup().getSequences(null);
     idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
-            selection);
+            selection, false);
 
     idGraphics.setFont(av.getFont());
     idGraphics.translate(0, -scaleHeight);
@@ -1053,7 +1088,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       int offset = getAlabels().getScrollOffset();
       idGraphics.translate(0, -offset);
       idGraphics.translate(0, alignmentDrawnHeight);
-      getAlabels().drawComponent(idGraphics, idWidth);
+      getAlabels().drawComponentNotGUI(idGraphics, idWidth);
       idGraphics.translate(0, -alignmentDrawnHeight);
 
       /*
@@ -1134,7 +1169,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * draw sequence ids and annotation labels (if shown)
      */
     IdCanvas idCanvas = getIdPanel().getIdCanvas();
-    idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight);
+    idCanvas.drawIdsWrappedNoGUI((Graphics2D) g, av, 0, totalHeight);
 
     g.translate(idWidth, 0);
 
@@ -1186,6 +1221,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
 
     int w = getIdPanel().getWidth();
+    w = this.calculateIdWidth(-1, true, true).width;
     return (w > 0 ? w : calculateIdWidth().width);
   }
 
@@ -1211,6 +1247,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     final int borderBottomOffset = 5;
 
     AlignmentDimension aDimension = getAlignmentDimension();
+
     // todo use a lambda function in place of callback here?
     ImageWriterI writer = new ImageWriterI()
     {
@@ -1424,8 +1461,7 @@ 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