*/
package jalview.gui;
-import jalview.analysis.AlignSeq;
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileFormat;
-import jalview.io.FormatAdapter;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
import java.awt.Color;
import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.awt.geom.AffineTransform;
+import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
+import java.util.Locale;
+import java.util.concurrent.Callable;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenuItem;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentUtils;
+import jalview.bin.Console;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.GroupSet;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.io.NewickFile;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
+
/**
* The panel that holds the labels for alignment annotations, providing
* tooltips, context menus, drag to reorder rows, and drag to adjust panel
*/
public AnnotationLabels(AlignmentPanel ap)
{
+
this.ap = ap;
av = ap.av;
ToolTipManager.sharedInstance().registerComponent(this);
AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
- boolean fullRepaint = false;
- if (evt.getActionCommand().equals(ADDNEW))
+ String action = evt.getActionCommand();
+ if (ADDNEW.equals(action))
{
+ /*
+ * non-returning dialog
+ */
AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
null, new Annotation[ap.av.getAlignment().getWidth()]);
-
- if (!editLabelDescription(newAnnotation))
- {
- return;
- }
-
- ap.av.getAlignment().addAnnotation(newAnnotation);
- ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
- fullRepaint = true;
+ editLabelDescription(newAnnotation, true);
}
- else if (evt.getActionCommand().equals(EDITNAME))
+ else if (EDITNAME.equals(action))
{
- String name = aa[selectedRow].label;
- editLabelDescription(aa[selectedRow]);
- if (!name.equalsIgnoreCase(aa[selectedRow].label))
- {
- fullRepaint = true;
- }
+ /*
+ * non-returning dialog
+ */
+ editLabelDescription(aa[selectedRow], false);
}
- else if (evt.getActionCommand().equals(HIDE))
+ else if (HIDE.equals(action))
{
aa[selectedRow].visible = false;
}
- else if (evt.getActionCommand().equals(DELETE))
+ else if (DELETE.equals(action))
{
ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
- fullRepaint = true;
}
- else if (evt.getActionCommand().equals(SHOWALL))
+ else if (SHOWALL.equals(action))
{
for (int i = 0; i < aa.length; i++)
{
aa[i].visible = true;
}
}
- fullRepaint = true;
}
- else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+ else if (OUTPUT_TEXT.equals(action))
{
new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]);
}
- else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+ else if (COPYCONS_SEQ.equals(action))
{
SequenceI cons = null;
if (aa[selectedRow].groupRef != null)
{
copy_annotseqtoclipboard(cons);
}
-
}
- else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
+ else if (TOGGLE_LABELSCALE.equals(action))
{
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
- ap.refresh(fullRepaint);
-
+ ap.refresh(true);
}
/**
- * DOCUMENT ME!
+ * Shows a dialog where the annotation name and description may be edited. If
+ * parameter addNew is true, then on confirmation, a new AlignmentAnnotation
+ * is added, else an existing annotation is updated.
*
- * @param e
- * DOCUMENT ME!
+ * @param annotation
+ * @param addNew
*/
- boolean editLabelDescription(AlignmentAnnotation annotation)
+ void editLabelDescription(AlignmentAnnotation annotation, boolean addNew)
{
- // TODO i18n
+ String name = MessageManager.getString("label.annotation_name");
+ String description = MessageManager
+ .getString("label.annotation_description");
+ String title = MessageManager
+ .getString("label.edit_annotation_name_description");
EditNameDialog dialog = new EditNameDialog(annotation.label,
- annotation.description, " Annotation Name ",
- "Annotation Description ", "Edit Annotation Name/Description",
- ap.alignFrame);
-
- if (!dialog.accept)
- {
- return false;
- }
-
- annotation.label = dialog.getName();
+ annotation.description, name, description);
- String text = dialog.getDescription();
- if (text != null && text.length() == 0)
- {
- text = null;
- }
- annotation.description = text;
-
- return true;
+ dialog.showDialog(ap.alignFrame, title, () -> {
+ annotation.label = dialog.getName();
+ String text = dialog.getDescription();
+ if (text != null && text.length() == 0)
+ {
+ text = null;
+ }
+ annotation.description = text;
+ if (addNew)
+ {
+ ap.av.getAlignment().addAnnotation(annotation);
+ ap.av.getAlignment().setAnnotationIndex(annotation, 0);
+ }
+ ap.refresh(true);
+ return null;
+ });
}
@Override
consclipbrd.addActionListener(this);
pop.add(consclipbrd);
}
- }
+
+ addColourOrFilterByOptions(ap,aa[selectedRow],pop);
+
+ if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP)
+ {
+ addContactMatrixOptions(ap,aa[selectedRow],pop);
+ // Set/adjust threshold for grouping ?
+ // colour alignment by this [type]
+ // select/hide columns by this row
+
+ }
+ }
+
pop.show(this, evt.getX(), evt.getY());
}
+ static void addColourOrFilterByOptions(final AlignmentPanel ap,
+ final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+ {
+ JMenuItem item;
+ item = new JMenuItem(MessageManager.getString("label.colour_by_annotation"));
+ item.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,false);
+ };
+ });
+ pop.add(item);
+ if (alignmentAnnotation.sequenceRef!=null)
+ {
+ item = new JMenuItem(MessageManager.getString("label.colour_by_annotation")+" ("+MessageManager.getString("label.per_seq")+")");
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,true);
+ };
+ });
+ pop.add(item);
+ }
+ item = new JMenuItem(MessageManager.getString("action.select_by_annotation"));
+ item.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AnnotationColumnChooser.displayFor(ap.av,ap,alignmentAnnotation);
+ };
+ });
+ pop.add(item);
+ }
+ static void addContactMatrixOptions(final AlignmentPanel ap,
+ final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+ {
+
+ final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation);
+ JMenuItem item;
+ if (cm != null)
+ {
+ pop.addSeparator();
+
+ if (cm.hasGroups())
+ {
+ JCheckBoxMenuItem chitem = new JCheckBoxMenuItem("Show Groups on Matrix");
+ boolean showGroups = alignmentAnnotation.isShowGroupsForContactMatrix();
+ final AlignmentAnnotation sel_row=alignmentAnnotation;
+ chitem.setState(showGroups);
+ chitem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sel_row.setShowGroupsForContactMatrix(chitem.getState());
+ ap.getAnnotationPanel()
+ .paint(ap.getAnnotationPanel().getGraphics());
+ }
+ });
+ pop.add(chitem);
+ }
+ if (cm.hasTree())
+ {
+ item = new JMenuItem("Show Tree for Matrix");
+ item.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+
+ ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
+
+ }
+ });
+ pop.add(item);
+ }
+ else
+ {
+ item = new JMenuItem("Calculate Tree for Matrix");
+ item.addActionListener(new ActionListener()
+ {
+ // TODO - refactor to analysis background thread
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ AlignmentAnnotation alan = alignmentAnnotation;
+ cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true));
+ ap.alignFrame.showContactMapTree(alan, cm);
+ }
+ }).start();
+ }
+ });
+ pop.add(item);
+ }
+ }
+ }
+
/**
* A helper method that adds menu options for calculation and visualisation of
* group and/or alignment consensus annotation to a popup menu. This is
* @param pop
*/
static void addConsensusMenuOptions(AlignmentPanel ap,
- AlignmentAnnotation ann,
- JPopupMenu pop)
+ AlignmentAnnotation ann, JPopupMenu pop)
{
pop.addSeparator();
if (selectedRow > -1 && ap.av.getAlignment()
.getAlignmentAnnotation().length > selectedRow)
{
- AlignmentAnnotation aa = ap.av.getAlignment()
- .getAlignmentAnnotation()[selectedRow];
+ AlignmentAnnotation[] anns = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ AlignmentAnnotation aa = anns[selectedRow];
String desc = getTooltip(aa);
this.setToolTipText(desc);
- ap.alignFrame.setStatus(aa.label);
+ String msg = getStatusMessage(aa, anns);
+ ap.alignFrame.setStatus(msg);
}
}
/**
+ * Constructs suitable text to show in the status bar when over an annotation
+ * label, containing the associated sequence name (if any), and the annotation
+ * labels (or all labels for a graph group annotation)
+ *
+ * @param aa
+ * @param anns
+ * @return
+ */
+ static String getStatusMessage(AlignmentAnnotation aa,
+ AlignmentAnnotation[] anns)
+ {
+ if (aa == null)
+ {
+ return null;
+ }
+
+ StringBuilder msg = new StringBuilder(32);
+ if (aa.sequenceRef != null)
+ {
+ msg.append(aa.sequenceRef.getName()).append(" : ");
+ }
+
+ if (aa.graphGroup == -1)
+ {
+ msg.append(aa.label);
+ }
+ else if (anns != null)
+ {
+ boolean first = true;
+ for (int i = anns.length - 1; i >= 0; i--)
+ {
+ if (anns[i].graphGroup == aa.graphGroup)
+ {
+ if (!first)
+ {
+ msg.append(", ");
+ }
+ msg.append(anns[i].label);
+ first = false;
+ }
+ }
+ }
+
+ return msg.toString();
+ }
+
+ /**
* Answers a tooltip, formatted as html, containing the annotation description
* (prefixed by associated sequence id if applicable), and the annotation
* (non-positional) score if it has one. Answers null if neither description
// jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
// tooltips
String desc = aa.getDescription(true).trim();
- if (!desc.toLowerCase().startsWith(HTML_START_TAG))
+ if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG))
{
tooltip.append(HTML_START_TAG);
desc = desc.replace("<", "<");
}
- else if (desc.toLowerCase().endsWith(HTML_END_TAG))
+ else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG))
{
desc = desc.substring(0, desc.length() - HTML_END_TAG.length());
}
protected void showOrHideAdjuster(MouseEvent evt)
{
boolean was = resizePanel;
- resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+ resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
+ && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
if (resizePanel != was)
{
- setCursor(Cursor.getPredefinedCursor(
- resizePanel ? Cursor.S_RESIZE_CURSOR
+ setCursor(Cursor
+ .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR
: Cursor.DEFAULT_CURSOR));
repaint();
}
int width = getWidth();
if (width == 0)
{
- width = ap.calculateIdWidth().width + 4;
+ width = ap.calculateIdWidth().width;
}
Graphics2D g2 = (Graphics2D) g;
g.translate(0, getScrollOffset());
g.setColor(Color.black);
-
+ SequenceI lastSeqRef = null;
+ String lastLabel = null;
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int fontHeight = g.getFont().getSize();
int y = 0;
{
hasHiddenRows = false;
int olY = 0;
+ int nexAA = 0;
for (int i = 0; i < aa.length; i++)
{
visible = true;
continue;
}
olY = y;
+ // look ahead to next annotation
+ for (nexAA = i + 1; nexAA < aa.length
+ && !aa[nexAA].visible; nexAA++)
+ ;
y += aa[i].height;
if (clip)
{
{
offset += fm.getDescent();
}
-
- x = width - fm.stringWidth(aa[i].label) - 3;
+ String label = aa[i].label;
+ boolean vertBar = false;
+ if ((lastLabel != null && lastLabel.equals(label)))
+ {
+ label = aa[i].description;
+ }
+ else
+ {
+ if (nexAA < aa.length && label.equals(aa[nexAA].label)) // &&
+ // aa[nexY].sequenceRef==aa[i].sequenceRef)
+ {
+ lastLabel = label;
+ // next label is the same as this label
+ label = aa[i].description;
+ }
+ else
+ {
+ lastLabel = label;
+ }
+ }
+ if (aa[i].sequenceRef != null)
+ {
+ if (aa[i].sequenceRef != lastSeqRef)
+ {
+ label = aa[i].sequenceRef.getName() + " " + label;
+ // TODO record relationship between sequence and this annotation and
+ // display it here
+ }
+ else
+ {
+ vertBar = true;
+ }
+ }
+ x = width - fm.stringWidth(label) - 3;
if (aa[i].graphGroup > -1)
{
}
else
{
- g.drawString(aa[i].label, x, y + offset);
+ if (vertBar)
+ {
+ g.drawLine(width - 3, y + offset - fontHeight, width - 3,
+ (int) (y - 1.5 * aa[i].height - offset - fontHeight));
+ // g.drawLine(20, y + offset, x - 20, y + offset);
+
+ }
+ g.drawString(label, x, y + offset);
}
+ lastSeqRef = aa[i].sequenceRef;
}
}
if (!resizePanel && dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
- g.drawString(aa[selectedRow].label, dragEvent.getX(),
- dragEvent.getY() - getScrollOffset());
+ g.drawString(
+ (aa[selectedRow].sequenceRef == null ? ""
+ : aa[selectedRow].sequenceRef.getName())
+ + aa[selectedRow].label,
+ dragEvent.getX(), dragEvent.getY() - getScrollOffset());
}
if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
git://source.jalview.org / jalview.git / blobdiff