*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
public class AnnotationPanel extends Panel implements AwtRenderPanelI,
AdjustmentListener, ActionListener, MouseListener,
int activeRow = -1;
- Vector activeRes;
-
final String HELIX = "Helix";
final String SHEET = "Sheet";
public AnnotationPanel(AlignmentPanel ap)
{
- MAC = new jalview.util.Platform().isAMac();
+ new jalview.util.Platform();
+ MAC = Platform.isAMac();
this.ap = ap;
av = ap.av;
setLayout(null);
String label = "";
if (av.getColumnSelection() != null
- && av.getColumnSelection().size() > 0
+ && !av.getColumnSelection().isEmpty()
&& anot[av.getColumnSelection().getMin()] != null)
+ {
label = anot[av.getColumnSelection().getMin()].displayCharacter;
+ }
if (evt.getActionCommand().equals(REMOVE))
{
- for (int i = 0; i < av.getColumnSelection().size(); i++)
+ for (int index : av.getColumnSelection().getSelected())
{
- anot[av.getColumnSelection().columnAt(i)] = null;
+ if (av.getColumnSelection().isVisible(index))
+ {
+ anot[index] = null;
+ }
}
}
else if (evt.getActionCommand().equals(LABEL))
aa[activeRow].hasText = true;
}
- for (int i = 0; i < av.getColumnSelection().size(); i++)
+ for (int index : av.getColumnSelection().getSelected())
{
- int index = av.getColumnSelection().columnAt(i);
-
+ // TODO: JAL-2001 - provide a fast method to list visible selected
+ // columns
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
Color col = udc.getColor();
- for (int i = 0; i < av.getColumnSelection().size(); i++)
+ for (int index : av.getColumnSelection().getSelected())
{
- int index = av.getColumnSelection().columnAt(i);
-
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
else if (evt.getActionCommand().equals(STEM))
{
type = 'S';
- symbol = "\u03C3";
+ int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+ symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
}
if (!aa[activeRow].hasIcons)
}
}
- for (int i = 0; i < av.getColumnSelection().size(); i++)
+ for (int index : av.getColumnSelection().getSelected())
{
- int index = av.getColumnSelection().columnAt(i);
-
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
anot[index] = new Annotation(label, "", type, 0);
}
-
anot[index].secondaryStructure = type != 'S' ? type : label
.length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
ap.alignFrame, "Enter Label", 400, 200, true);
if (dialog.accept)
+ {
return dialog.getName();
+ }
else
+ {
return null;
+ }
}
@Override
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
&& activeRow != -1)
{
- if (av.getColumnSelection() == null)
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().isEmpty())
{
return;
}
PopupMenu pop = new PopupMenu(
MessageManager.getString("label.structure_type"));
MenuItem item;
- /*
- * Just display the needed structure options
- */
- if (av.getAlignment().isNucleotide() == true)
+
+ if (av.getAlignment().isNucleotide())
{
item = new MenuItem(STEM);
item.addActionListener(this);
return;
}
- if (aa == null)
- {
- return;
- }
-
ap.scalePanel.mousePressed(evt);
}
}
}
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+ int column = evt.getX() / av.getCharWidth() + av.getStartRes();
if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ column = av.getColumnSelection().adjustForHiddenColumns(column);
}
- if (row > -1 && res < aa[row].annotations.length
- && aa[row].annotations[res] != null)
+ if (row > -1 && column < aa[row].annotations.length
+ && aa[row].annotations[column] != null)
{
- StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
- if (aa[row].annotations[res].description != null)
+ StringBuilder text = new StringBuilder();
+ text.append(MessageManager.getString("label.column")).append(" ")
+ .append(column + 1);
+ String description = aa[row].annotations[column].description;
+ if (description != null && description.length() > 0)
{
- text.append(" " + aa[row].annotations[res].description);
+ text.append(" ").append(description);
}
+
+ /*
+ * if the annotation is sequence-specific, show the sequence number
+ * in the alignment, and (if not a gap) the residue and position
+ */
+ SequenceI seqref = aa[row].sequenceRef;
+ if (seqref != null)
+ {
+ int seqIndex = av.getAlignment().findIndex(seqref);
+ if (seqIndex != -1)
+ {
+ text.append(", ")
+ .append(MessageManager.getString("label.sequence"))
+ .append(" ").append(seqIndex + 1);
+ char residue = seqref.getCharAt(column);
+ if (!Comparison.isGap(residue))
+ {
+ text.append(" ");
+ String name;
+ if (av.getAlignment().isNucleotide())
+ {
+ name = ResidueProperties.nucleotideName.get(String
+ .valueOf(residue));
+ text.append(" Nucleotide: ").append(
+ name != null ? name : residue);
+ }
+ else
+ {
+ name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+ : ResidueProperties.aa2Triplet.get(String
+ .valueOf(residue)));
+ text.append(" Residue: ").append(
+ name != null ? name : residue);
+ }
+ int residuePos = seqref.findPosition(column);
+ text.append(" (").append(residuePos).append(")");
+ // int residuePos = seqref.findPosition(column);
+ // text.append(residue).append(" (")
+ // .append(residuePos).append(")");
+ }
+ }
+ }
+
ap.alignFrame.statusBar.setText(text.toString());
}
}
}
}
}
-
- if (activeRes == null)
- {
- activeRes = new Vector();
- activeRes.addElement(String.valueOf(i));
- return;
- }
-
- activeRes.addElement(String.valueOf(i));
}
@Override
return;
}
- gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal
- * av.charWidth, 0);
+ gg.copyArea(0, 0, imgWidth, getSize().height,
+ -horizontal * av.getCharWidth(), 0);
int sr = av.startRes, er = av.endRes + 1, transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * av.getCharWidth();
sr = er - horizontal;
}
else if (horizontal < 0)
g.setFont(ofont);
g.setColor(Color.white);
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
+ g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(),
+ getSize().height);
if (fm == null)
{
return bounds;
}
else
+ {
return null;
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff