*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.api.AlignViewportI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.SelectionListener;
import jalview.structure.SelectionSource;
import jalview.structure.SequenceListener;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Vector;
+
public class SeqPanel extends Panel implements MouseMotionListener,
- MouseListener, SequenceListener
+ MouseListener, SequenceListener, SelectionListener
{
public SeqCanvas seqCanvas;
seqCanvas.addMouseListener(this);
ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
seqCanvas.repaint();
}
void setCursorPosition()
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
- seqCanvas.cursorY);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
scrollToVisible();
}
endEditing();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
ap.scrollToWrappedVisible(seqCanvas.cursorX);
}
void setSelectionAreaAtCursor(boolean topLeft)
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
- seqCanvas.cursorY);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
{
int res = 0;
int x = evt.getX();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap
+ seqCanvas.getAnnotationHeight();
int y = evt.getY();
int seq = 0;
int y = evt.getY();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap
+ seqCanvas.getAnnotationHeight();
y -= hgap;
{
String tmp = sequence.hashCode() + index + "";
if (lastMessage == null || !lastMessage.equals(tmp))
+ {
ssm.mouseOverSequence(sequence, index, pos, av);
+ }
lastMessage = tmp;
}
}
+ @Override
+ public VamsasSource getVamsasSource()
+ {
+ return this.ap == null ? null : this.ap.av;
+ }
+
public void updateColours(SequenceI seq, int index)
{
System.out.println("update the seqPanel colours");
int respos = sequence.findPosition(res);
if (ssm != null)
+ {
mouseOverSequence(sequence, res, respos);
+ }
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
- + sequence.getName());
+ StringBuilder text = new StringBuilder();
+ text.append("Sequence ").append(Integer.toString(seq + 1))
+ .append(" ID: ").append(sequence.getName());
- Object obj = null;
+ String obj = null;
+ final String ch = String.valueOf(sequence.getCharAt(res));
if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
- + "");
+ obj = ResidueProperties.nucleotideName.get(ch);
if (obj != null)
{
- text.append(" Nucleotide: ");
+ text.append(" Nucleotide: ").append(obj);
}
}
else
{
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+ obj = "X".equalsIgnoreCase(ch) ? "STOP"
+ : ResidueProperties.aa2Triplet.get(ch);
if (obj != null)
{
- text.append(" Residue: ");
+ text.append(" Residue: ").append(obj);
}
}
if (obj != null)
{
- if (obj != "")
- {
- text.append(obj + " (" + respos + ")");
- }
+ text.append(" (").append(Integer.toString(respos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
- StringBuffer tooltipText = new StringBuffer();
+ StringBuilder tooltipText = new StringBuilder();
SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
if (groups != null)
{
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
{
- tooltipText.append(groups[g].getName() + " ");
+ tooltipText.append(groups[g].getName()).append(" ");
}
if (groups[g].getDescription() != null)
{
{
if (mouseWheelPressed)
{
- int oldWidth = av.charWidth;
+ int oldWidth = av.getCharWidth();
// Which is bigger, left-right or up-down?
if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
{
int fontSize = av.font.getSize();
- if (evt.getY() < lastMousePress.y && av.charHeight > 1)
+ if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)
{
fontSize--;
}
}
av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
- av.charWidth = oldWidth;
+ av.setCharWidth(oldWidth);
}
else
{
- if (evt.getX() < lastMousePress.x && av.charWidth > 1)
+ if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1)
{
- av.charWidth--;
+ av.setCharWidth(av.getCharWidth() - 1);
}
else if (evt.getX() > lastMousePress.x)
{
- av.charWidth++;
+ av.setCharWidth(av.getCharWidth() + 1);
}
- if (av.charWidth < 1)
+ if (av.getCharWidth() < 1)
{
- av.charWidth = 1;
+ av.setCharWidth(1);
}
}
ap.fontChanged();
FontMetrics fm = getFontMetrics(av.getFont());
- av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+ av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
lastMousePress = evt.getPoint();
{
if (av.isHiddenRepSequence(seq))
{
- sg = (SequenceGroup) av.getRepresentedSequences(seq);
+ sg = av.getRepresentedSequences(seq);
groupEditing = true;
}
}
StringBuffer message = new StringBuffer();
if (groupEditing)
{
- message.append(MessageManager.getString("action.edit_group")).append(":");
+ message.append(MessageManager.getString("action.edit_group")).append(
+ ":");
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
+ editCommand = new EditCommand(
+ MessageManager.getString("action.edit_group"));
}
}
else
{
- message.append(MessageManager.getString("label.edit_sequence")).append(" " + seq.getName());
+ message.append(MessageManager.getString("label.edit_sequence"))
+ .append(" " + seq.getName());
String label = seq.getName();
if (label.length() > 10)
{
}
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
+ editCommand = new EditCommand(MessageManager.formatMessage(
+ "label.edit_params", new String[]
+ { label }));
}
}
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
- startres, startres - lastres, av.getAlignment(), true);
+ editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres,
+ startres - lastres, av.getAlignment(), true);
}
}
else
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
- startres, lastres - startres, av.getAlignment(), true);
+ editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+ lastres - startres, av.getAlignment(), true);
}
}
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+ editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
{ seq }, lastres, startres - lastres, av.getAlignment(), true);
}
}
if (max > 0)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
+ editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
{ seq }, startres, max, av.getAlignment(), true);
}
}
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+ editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1,
- av.getAlignment(), true);
+ editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
+ true);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1,
- av.getAlignment(), true);
+ editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),
+ true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+ editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
av.getAlignment(), true);
}
return;
}
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
if (sequence == null || res > sequence.getLength())
{
{
return;
}
+
+ /*
+ * Check for selection in a view of which this one is a dna/protein
+ * complement.
+ */
+ if (selectionFromTranslation(seqsel, colsel, source))
+ {
+ return;
+ }
+
// do we want to thread this ? (contention with seqsel and colsel locks, I
// suspect)
// rules are: colsel is copied if there is a real intersection between
ap.scrollTo(column, column, ap.av.startSeq, true, true);
}
+ /**
+ * If this panel is a cdna/protein translation view of the selection source,
+ * tries to map the source selection to a local one, and returns true. Else
+ * returns false.
+ *
+ * @param seqsel
+ * @param colsel
+ * @param source
+ */
+ protected boolean selectionFromTranslation(SequenceGroup seqsel,
+ ColumnSelection colsel, SelectionSource source)
+ {
+ if (!(source instanceof AlignViewportI)) {
+ return false;
+ }
+ final AlignViewportI sourceAv = (AlignViewportI) source;
+ if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv)
+ {
+ return false;
+ }
+
+ /*
+ * Map sequence selection
+ */
+ SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
+ av.setSelectionGroup(sg);
+ av.isSelectionGroupChanged(true);
+
+ /*
+ * Map column selection
+ */
+ ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+ av);
+ av.setColumnSelection(cs);
+ av.isColSelChanged(true);
+
+ firePropertyChange("alignment", null, av.getAlignment().getSequences());
+ // PaintRefresher.Refresh(this, av.getSequenceSetId());
+
+ return true;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff