X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=8a3138d179f7b8f7eb70038a0650636d94ed9bcc;hb=b636f0007e76155876da1dd75310a4cb153815d7;hp=568062b790a6bde5af2ea7dce3a8ec9e68d3f9bd;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 568062b..8a3138d 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,14 +20,29 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.ToolTipManager;
+
 /**
  * DOCUMENT ME!
  * 
@@ -70,6 +85,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
@@ -92,111 +108,138 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     min = res;
     max = res;
 
-    if (SwingUtilities.isRightMouseButton(evt))
+    if (evt.isPopupTrigger())
+    {
+      rightMouseButtonPressed(evt, res);
+    }
+    else
+    {
+      leftMouseButtonPressed(evt, res);
+    }
+  }
+
+  /**
+   * Handles right mouse button press. If pressed in a selected column, opens
+   * context menu for 'Hide Columns'. If pressed on a hidden columns marker,
+   * opens context menu for 'Reveal / Reveal All'. Else does nothing.
+   * 
+   * @param evt
+   * @param res
+   */
+  protected void rightMouseButtonPressed(MouseEvent evt, final int res)
+  {
+    JPopupMenu pop = new JPopupMenu();
+    if (reveal != null)
     {
-      JPopupMenu pop = new JPopupMenu();
-      if (reveal != null)
+      JMenuItem item = new JMenuItem(
+              MessageManager.getString("label.reveal"));
+      item.addActionListener(new ActionListener()
       {
-        JMenuItem item = new JMenuItem(
-                MessageManager.getString("label.reveal"));
-        item.addActionListener(new ActionListener()
+        @Override
+        public void actionPerformed(ActionEvent e)
         {
-          public void actionPerformed(ActionEvent e)
+          av.showColumn(reveal[0]);
+          reveal = null;
+          ap.paintAlignment(true);
+          if (ap.overviewPanel != null)
           {
-            av.showColumn(reveal[0]);
-            reveal = null;
-            ap.paintAlignment(true);
-            if (ap.overviewPanel != null)
-            {
-              ap.overviewPanel.updateOverviewImage();
-            }
+            ap.overviewPanel.updateOverviewImage();
           }
-        });
-        pop.add(item);
-
-        if (av.getColumnSelection().getHiddenColumns().size() > 1)
-        {
-          item = new JMenuItem(
-                  MessageManager.getString("action.reveal_all"));
-          item.addActionListener(new ActionListener()
-          {
-            public void actionPerformed(ActionEvent e)
-            {
-              av.showAllHiddenColumns();
-              reveal = null;
-              ap.paintAlignment(true);
-              if (ap.overviewPanel != null)
-              {
-                ap.overviewPanel.updateOverviewImage();
-              }
-            }
-          });
-          pop.add(item);
+          av.sendSelection();
         }
-        pop.show(this, evt.getX(), evt.getY());
-      }
-      else if (av.getColumnSelection().contains(res))
+      });
+      pop.add(item);
+
+      if (av.getColumnSelection().hasHiddenColumns())
       {
-        JMenuItem item = new JMenuItem(
-                MessageManager.getString("label.hide_columns"));
+        item = new JMenuItem(MessageManager.getString("action.reveal_all"));
         item.addActionListener(new ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent e)
           {
-            av.hideColumns(res, res);
-            if (av.getSelectionGroup() != null
-                    && av.getSelectionGroup().getSize() == av
-                            .getAlignment().getHeight())
-            {
-              av.setSelectionGroup(null);
-            }
-
+            av.showAllHiddenColumns();
+            reveal = null;
             ap.paintAlignment(true);
             if (ap.overviewPanel != null)
             {
               ap.overviewPanel.updateOverviewImage();
             }
+            av.sendSelection();
           }
         });
         pop.add(item);
-        pop.show(this, evt.getX(), evt.getY());
       }
+      pop.show(this, evt.getX(), evt.getY());
     }
-    else
-    // LEFT MOUSE TO SELECT
+    else if (av.getColumnSelection().contains(res))
     {
-      if (!evt.isControlDown() && !evt.isShiftDown())
+      JMenuItem item = new JMenuItem(
+              MessageManager.getString("label.hide_columns"));
+      item.addActionListener(new ActionListener()
       {
-        av.getColumnSelection().clear();
-      }
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.hideColumns(res, res);
+          if (av.getSelectionGroup() != null
+                  && av.getSelectionGroup().getSize() == av.getAlignment()
+                          .getHeight())
+          {
+            av.setSelectionGroup(null);
+          }
 
-      av.getColumnSelection().addElement(res);
-      SequenceGroup sg = new SequenceGroup();
-      // try to be as quick as possible
-      SequenceI[] iVec = av.getAlignment().getSequencesArray();
-      for (int i = 0; i < iVec.length; i++)
-      {
-        sg.addSequence(iVec[i], false);
-        iVec[i] = null;
-      }
-      iVec = null;
-      sg.setStartRes(res);
-      sg.setEndRes(res);
+          ap.paintAlignment(true);
+          if (ap.overviewPanel != null)
+          {
+            ap.overviewPanel.updateOverviewImage();
+          }
+          av.sendSelection();
+        }
+      });
+      pop.add(item);
+      pop.show(this, evt.getX(), evt.getY());
+    }
+  }
+
+  /**
+   * Handles left mouse button press
+   * 
+   * @param evt
+   * @param res
+   */
+  protected void leftMouseButtonPressed(MouseEvent evt, final int res)
+  {
+    if (!evt.isControlDown() && !evt.isShiftDown())
+    {
+      av.getColumnSelection().clear();
+    }
+
+    av.getColumnSelection().addElement(res);
+    SequenceGroup sg = new SequenceGroup();
+    // try to be as quick as possible
+    SequenceI[] iVec = av.getAlignment().getSequencesArray();
+    for (int i = 0; i < iVec.length; i++)
+    {
+      sg.addSequence(iVec[i], false);
+      iVec[i] = null;
+    }
+    iVec = null;
+    sg.setStartRes(res);
+    sg.setEndRes(res);
 
-      if (evt.isShiftDown())
+    if (evt.isShiftDown())
+    {
+      int min = Math.min(av.getColumnSelection().getMin(), res);
+      int max = Math.max(av.getColumnSelection().getMax(), res);
+      for (int i = min; i < max; i++)
       {
-        int min = Math.min(av.getColumnSelection().getMin(), res);
-        int max = Math.max(av.getColumnSelection().getMax(), res);
-        for (int i = min; i < max; i++)
-        {
-          av.getColumnSelection().addElement(i);
-        }
-        sg.setStartRes(min);
-        sg.setEndRes(max);
+        av.getColumnSelection().addElement(i);
       }
-      av.setSelectionGroup(sg);
+      sg.setStartRes(min);
+      sg.setEndRes(max);
     }
-
+    av.setSelectionGroup(sg);
     ap.paintAlignment(false);
     av.sendSelection();
   }
@@ -207,6 +250,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     mouseDragging = false;
@@ -254,6 +298,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     mouseDragging = true;
@@ -323,6 +368,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     }
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
     if (mouseDragging)
@@ -331,6 +377,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     }
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
     if (mouseDragging)
@@ -339,10 +386,12 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     }
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     if (!av.hasHiddenColumns())
@@ -355,25 +404,24 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     res = av.getColumnSelection().adjustForHiddenColumns(res);
 
     reveal = null;
-    for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+    if (av.getColumnSelection().getHiddenColumns() != null)
     {
-      int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
-              .elementAt(i);
-      if (res + 1 == region[0] || res - 1 == region[1])
-      {
-        reveal = region;
-        ToolTipManager.sharedInstance().registerComponent(this);
-        this.setToolTipText(MessageManager
-                .getString("label.reveal_hidden_columns"));
-        break;
-      }
-      else
+      for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
-        this.setToolTipText(null);
+        if (res + 1 == region[0] || res - 1 == region[1])
+        {
+          reveal = region;
+          ToolTipManager.sharedInstance().registerComponent(this);
+          this.setToolTipText(MessageManager
+                  .getString("label.reveal_hidden_columns"));
+          break;
+        }
+        else
+        {
+          this.setToolTipText(null);
+        }
       }
-
     }
-
     repaint();
   }
 
@@ -385,6 +433,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
     drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());
@@ -410,14 +459,18 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     // Fill the selected columns
     ColumnSelection cs = av.getColumnSelection();
+    int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
+
     int s;
     if (cs != null)
     {
       gg.setColor(new Color(220, 0, 0));
 
-      for (int i = 0; i < cs.size(); i++)
+      for (int sel : cs.getSelected())
       {
-        int sel = cs.columnAt(i);
+        // TODO: JAL-2001 - provide a fast method to list visible selected in a
+        // given range
+
         if (av.hasHiddenColumns())
         {
           if (cs.isVisible(sel))
@@ -432,90 +485,167 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
         if ((sel >= startx) && (sel <= endx))
         {
-          gg.fillRect((sel - startx) * av.charWidth, 0, av.charWidth,
+          gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth,
                   getHeight());
         }
       }
     }
-    // Draw the scale numbers
-    gg.setColor(Color.black);
 
-    int scalestartx = (startx / 10) * 10;
+    int widthx = 1 + endx - startx;
 
     FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = av.charHeight - fm.getDescent();
-
-    if ((scalestartx % 10) == 0)
-    {
-      scalestartx += 5;
-    }
-
-    String string;
-    int maxX = 0;
-
-    for (int i = scalestartx; i < endx; i += 5)
-    {
-      if ((i % 10) == 0)
-      {
-        string = String.valueOf(av.getColumnSelection()
-                .adjustForHiddenColumns(i));
-        if ((i - startx - 1) * av.charWidth > maxX)
-        {
-          gg.drawString(string, (i - startx - 1) * av.charWidth, y);
-          maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
-        }
-
-        gg.drawLine(
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                y + 2,
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                y + (fm.getDescent() * 2));
-
-      }
-      else
-      {
-        gg.drawLine(
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                y + fm.getDescent(),
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
-                y + (fm.getDescent() * 2));
-      }
-    }
-
+    int y = avCharHeight, yOf = fm.getDescent();
+    y -= yOf;
     if (av.hasHiddenColumns())
     {
+      // draw any hidden column markers
       gg.setColor(Color.blue);
       int res;
-      if (av.getShowHiddenMarkers())
+      if (av.getShowHiddenMarkers()
+              && av.getColumnSelection().getHiddenColumns() != null)
       {
         for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
                 .size(); i++)
         {
-
           res = av.getColumnSelection().findHiddenRegionPosition(i)
                   - startx;
 
-          if (res < 0 || res > endx - scalestartx)
+          if (res < 0 || res > widthx)
           {
             continue;
           }
 
-          gg.fillPolygon(new int[]
-          { res * av.charWidth - av.charHeight / 4,
-              res * av.charWidth + av.charHeight / 4, res * av.charWidth },
-                  new int[]
-                  { y - av.charHeight / 2, y - av.charHeight / 2, y + 8 },
-                  3);
+          gg.fillPolygon(new int[] {
+              -1 + res * avCharWidth - avCharHeight / 4,
+              -1 + res * avCharWidth + avCharHeight / 4,
+              -1 + res * avCharWidth }, new int[] { y, y, y + 2 * yOf }, 3);
 
         }
       }
+    }
+    // Draw the scale numbers
+    gg.setColor(Color.black);
 
+    List<Object[]> marks = calculateMarks(startx, endx);
+    int maxX = 0;
+    for (Object[] mark : marks)
+    {
+      boolean major = Boolean.valueOf((Boolean) mark[0]);
+      int mpos = ((Integer) mark[1]).intValue(); // (i - startx - 1)
+      String mstring = (String) mark[2];
+      if (mstring != null)
+      {
+        if (mpos * avCharWidth > maxX)
+        {
+          gg.drawString(mstring, mpos * avCharWidth, y);
+          maxX = (mpos + 2) * avCharWidth + fm.stringWidth(mstring);
+        }
+      }
+      if (major)
+      {
+        gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + 2,
+                (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
+      }
+      else
+      {
+        gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + yOf,
+                (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
+      }
+    }
+    if (av.hasHiddenColumns())
+    {
       if (reveal != null && reveal[0] > startx && reveal[0] < endx)
       {
         gg.drawString(MessageManager.getString("label.reveal_columns"),
-                reveal[0] * av.charWidth, 0);
+                reveal[0] * avCharWidth, 0);
       }
     }
 
   }
+
+  /**
+   * calculate positions markers on the alignment ruler
+   * 
+   * @return List { Object { .. } } Boolean: true/false for major/minor mark,
+   *         Integer: marker position in alignment column coords, String: null
+   *         or a String to be rendered at the position.
+   */
+  public List<Object[]> calculateMarks(int startx, int endx)
+  {
+    new ArrayList<Object[]>();
+
+    int scalestartx = (startx / 10) * 10;
+
+    SequenceI refSeq = av.getAlignment().getSeqrep();
+    int refSp = 0, refEp = -1, refStart = 0, refEnd = -1, refStartI = 0, refEndI = -1;
+    if (refSeq != null)
+    {
+      // find bounds and set origin appopriately
+      // locate first visible position for this sequence
+      int[] refbounds = av.getColumnSelection()
+              .locateVisibleBoundsOfSequence(refSeq);
+
+      refSp = refbounds[0];
+      refEp = refbounds[1];
+      refStart = refbounds[2];
+      refEnd = refbounds[3];
+      refStartI = refbounds[4];
+      refEndI = refbounds[5];
+      scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
+    }
+
+
+    if (refSeq == null && scalestartx % 10 == 0)
+    {
+      scalestartx += 5;
+    }
+    List<Object[]> marks = new ArrayList<Object[]>();
+    String string;
+    int maxX = 0, refN, iadj;
+    // todo: add a 'reference origin column' to set column number relative to
+    for (int i = scalestartx; i < endx; i += 5)
+    {
+      Object[] amark = new Object[3];
+      if (((i - refSp) % 10) == 0)
+      {
+        if (refSeq == null)
+        {
+          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1) + 1;
+          string = String.valueOf(iadj);
+        }
+        else
+        {
+          iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1);
+          refN = refSeq.findPosition(iadj);
+          // TODO show bounds if position is a gap
+          // - ie L--R -> "1L|2R" for
+          // marker
+          if (iadj < refStartI)
+          {
+            string = String.valueOf(iadj - refStartI);
+          }
+          else if (iadj > refEndI)
+          {
+            string = "+" + String.valueOf(iadj - refEndI);
+          }
+          else
+          {
+            string = String.valueOf(refN) + refSeq.getCharAt(iadj);
+          }
+        }
+        amark[0] = Boolean.TRUE;
+        amark[1] = Integer.valueOf(i - startx - 1);
+        amark[2] = string;
+
+      }
+      else
+      {
+        amark[0] = Boolean.FALSE;
+        amark[1] = Integer.valueOf(i - startx - 1);
+        amark[2] = null;
+      }
+      marks.add(amark);
+    }
+    return marks;
+  }
 }