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 java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.awt.image.BufferedImage;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
boolean mouseDragging = false;
- boolean MAC = false;
-
// for editing cursor
int cursorX = 0;
*/
public AnnotationPanel(AlignmentPanel ap)
{
-
- MAC = jalview.util.Platform.isAMac();
-
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
String action = evt.getActionCommand();
if (action.equals(REMOVE))
{
- for (int sel : av.getColumnSelection().getSelected())
+ for (int index : av.getColumnSelection().getSelected())
{
- anot[sel] = null;
+ if (av.getColumnSelection().isVisible(index))
+ {
+ anot[index] = null;
+ }
}
}
else if (action.equals(LABEL))
return;
}
- private String collectAnnotVals(Annotation[] anot, String label2)
+ /**
+ * Returns any existing annotation concatenated as a string. For each
+ * annotation, takes the description, if any, else the secondary structure
+ * character (if type is HELIX, SHEET or STEM), else the display character (if
+ * type is LABEL).
+ *
+ * @param anots
+ * @param type
+ * @return
+ */
+ private String collectAnnotVals(Annotation[] anots, String type)
{
- String collatedInput = "";
+ // TODO is this method wanted? why? 'last' is not used
+
+ StringBuilder collatedInput = new StringBuilder(64);
String last = "";
ColumnSelection viscols = av.getColumnSelection();
- // TODO: refactor and save av.getColumnSelection for efficiency
- for (int index : viscols.getSelected())
+
+ /*
+ * the selection list (read-only view) is in selection order, not
+ * column order; make a copy so we can sort it
+ */
+ List<Integer> selected = new ArrayList<Integer>(viscols.getSelected());
+ Collections.sort(selected);
+ for (int index : selected)
{
// always check for current display state - just in case
if (!viscols.isVisible(index))
continue;
}
String tlabel = null;
- if (anot[index] != null)
+ if (anots[index] != null)
{ // LML added stem code
- if (label2.equals(HELIX) || label2.equals(SHEET)
- || label2.equals(STEM) || label2.equals(LABEL))
+ if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
+ || type.equals(LABEL))
{
- tlabel = anot[index].description;
+ tlabel = anots[index].description;
if (tlabel == null || tlabel.length() < 1)
{
- if (label2.equals(HELIX) || label2.equals(SHEET)
- || label2.equals(STEM))
+ if (type.equals(HELIX) || type.equals(SHEET)
+ || type.equals(STEM))
{
- tlabel = "" + anot[index].secondaryStructure;
+ tlabel = "" + anots[index].secondaryStructure;
}
else
{
- tlabel = "" + anot[index].displayCharacter;
+ tlabel = "" + anots[index].displayCharacter;
}
}
}
{
if (last.length() > 0)
{
- collatedInput += " ";
+ collatedInput.append(" ");
}
- collatedInput += tlabel;
+ collatedInput.append(tlabel);
}
}
}
- return collatedInput;
+ return collatedInput.toString();
}
/**
int height = 0;
activeRow = -1;
+ final int y = evt.getY();
for (int i = 0; i < aa.length; i++)
{
if (aa[i].visible)
height += aa[i].height;
}
- if (evt.getY() < height)
+ if (y < height)
{
if (aa[i].editable)
{
{
// Stretch Graph
graphStretch = i;
- graphStretchY = evt.getY();
+ graphStretchY = y;
}
break;
}
}
+ /*
+ * isPopupTrigger fires in mousePressed on Mac,
+ * not until mouseRelease on Windows
+ */
if (evt.isPopupTrigger() && activeRow != -1)
{
- if (av.getColumnSelection() == null
- || av.getColumnSelection().isEmpty())
- {
- return;
- }
+ showPopupMenu(y, evt.getX());
+ return;
+ }
- JPopupMenu pop = new JPopupMenu(
- MessageManager.getString("label.structure_type"));
- JMenuItem item;
- /*
- * Just display the needed structure options
- */
- if (av.getAlignment().isNucleotide())
- {
- item = new JMenuItem(STEM);
- item.addActionListener(this);
- pop.add(item);
- }
- else
- {
- item = new JMenuItem(HELIX);
- item.addActionListener(this);
- pop.add(item);
- item = new JMenuItem(SHEET);
- item.addActionListener(this);
- pop.add(item);
- }
- item = new JMenuItem(LABEL);
+ ap.getScalePanel().mousePressed(evt);
+ }
+
+ /**
+ * Construct and display a context menu at the right-click position
+ *
+ * @param y
+ * @param x
+ */
+ void showPopupMenu(final int y, int x)
+ {
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().isEmpty())
+ {
+ return;
+ }
+
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.structure_type"));
+ JMenuItem item;
+ /*
+ * Just display the needed structure options
+ */
+ if (av.getAlignment().isNucleotide())
+ {
+ item = new JMenuItem(STEM);
item.addActionListener(this);
pop.add(item);
- item = new JMenuItem(COLOUR);
+ }
+ else
+ {
+ item = new JMenuItem(HELIX);
item.addActionListener(this);
pop.add(item);
- item = new JMenuItem(REMOVE);
+ item = new JMenuItem(SHEET);
item.addActionListener(this);
pop.add(item);
- pop.show(this, evt.getX(), evt.getY());
-
- return;
}
-
- ap.getScalePanel().mousePressed(evt);
-
+ item = new JMenuItem(LABEL);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(COLOUR);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(REMOVE);
+ item.addActionListener(this);
+ pop.add(item);
+ pop.show(this, x, y);
}
/**
graphStretchY = -1;
mouseDragging = false;
ap.getScalePanel().mouseReleased(evt);
+
+ /*
+ * isPopupTrigger is set in mouseReleased on Windows
+ * (in mousePressed on Mac)
+ */
+ if (evt.isPopupTrigger() && activeRow != -1)
+ {
+ showPopupMenu(evt.getY(), evt.getX());
+ }
+
}
/**
{
text.append(", ")
.append(MessageManager.getString("label.sequence"))
- .append(" ")
- .append(seqIndex + 1);
+ .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(residue).append(" (")
- .append(residuePos).append(")");
+ text.append(" (").append(residuePos).append(")");
}
}
}
return null;
}
}
+
+ /**
+ * Try to ensure any references held are nulled
+ */
+ public void dispose()
+ {
+ av = null;
+ ap = null;
+ image = null;
+ fadedImage = null;
+ gg = null;
+ _mwl = null;
+
+ /*
+ * I created the renderer so I will dispose of it
+ */
+ if (renderer != null)
+ {
+ renderer.dispose();
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff