*/
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 jalview.workers.InformationThread;
-
import java.awt.Color;
import java.awt.Cursor;
import java.awt.Dimension;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
-import java.util.regex.Pattern;
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.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 jalview.workers.InformationThread;
+
/**
* The panel that holds the labels for alignment annotations, providing
* tooltips, context menus, drag to reorder rows, and drag to adjust panel
public class AnnotationLabels extends JPanel
implements MouseListener, MouseMotionListener, ActionListener
{
+ private static final String HTML_END_TAG = "</html>";
+
+ private static final String HTML_START_TAG = "<html>";
+
/**
* width in pixels within which height adjuster arrows are shown and active
*/
*/
private static int HEIGHT_ADJUSTER_HEIGHT = 10;
- private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
- .compile("<");
-
private static final Font font = new Font("Arial", Font.PLAIN, 11);
private static final String TOGGLE_LABELSCALE = MessageManager
*/
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.description, name, description);
- annotation.label = dialog.getName();
-
- String text = dialog.getDescription();
- if (text != null && text.length() == 0)
- {
- text = null;
- }
- annotation.description = text;
-
- return true;
+ dialog.showDialog(ap.alignFrame, title,
+ new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ 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);
+ }
+ });
}
@Override
// JAL-1264 hide all sequence-specific annotations of this type
if (selectedRow < aa.length)
{
- if (isSequenceAnnotation)
+ if (aa[selectedRow].sequenceRef != null)
{
- final String label = ann.label;
+ final String label = aa[selectedRow].label;
JMenuItem hideType = new JMenuItem();
String text = MessageManager.getString("label.hide_all") + " "
+ label;
// property methods
if (selectedRow < aa.length)
{
- final String label = ann.label;
- if (!(ann.autoCalculated)
+ final String label = aa[selectedRow].label;
+ if (!(aa[selectedRow].autoCalculated)
&& !(InformationThread.HMM_CALC_ID.equals(ann.getCalcId())))
{
- if (ann.graph == AlignmentAnnotation.NO_GRAPH)
+ if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
{
// display formatting settings for this row.
pop.addSeparator();
// av and sequencegroup need to implement same interface for
item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
- ann.scaleColLabel);
+ aa[selectedRow].scaleColLabel);
item.addActionListener(this);
pop.add(item);
}
}
else if (label.indexOf("Consensus") > -1)
{
- addConsensusMenu(pop, ann);
+ addConsensusMenuOptions(ap, aa[selectedRow], pop);
+
+ final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+ consclipbrd.addActionListener(this);
+ pop.add(consclipbrd);
}
else if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
{
}
/**
- * Adds context menu options for (alignment or group) Consensus annotation
+ * A helper method that adds menu options for calculation and visualisation of
+ * group and/or alignment consensus annotation to a popup menu. This is
+ * designed to be reusable for either unwrapped mode (popup menu is shown on
+ * component AnnotationLabels), or wrapped mode (popup menu is shown on
+ * IdPanel when the mouse is over an annotation label).
*
- * @param pop
+ * @param ap
* @param ann
+ * @param pop
*/
- protected void addConsensusMenu(JPopupMenu pop,
- final AlignmentAnnotation ann)
+ static void addConsensusMenuOptions(AlignmentPanel ap,
+ AlignmentAnnotation ann,
+ JPopupMenu pop)
{
- final boolean isGroupAnnotation = ann.groupRef != null;
pop.addSeparator();
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
MessageManager.getString("label.ignore_gaps_consensus"),
- (ann.groupRef != null)
- ? ann.groupRef.isIgnoreGapsConsensus()
+ (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus()
: ap.av.isIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = ann;
cbmi.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- if (isGroupAnnotation)
+ if (aaa.groupRef != null)
{
- ann.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+ aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+ ap.getAnnotationPanel()
+ .paint(ap.getAnnotationPanel().getGraphics());
}
else
{
}
});
pop.add(cbmi);
- if (isGroupAnnotation)
+
+ if (aaa.groupRef != null)
{
/*
* group consensus options
@Override
public void actionPerformed(ActionEvent e)
{
- ann.groupRef.setShowConsensusHistogram(chist.getState());
+ aaa.groupRef.setShowConsensusHistogram(chist.getState());
ap.repaint();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- ann.groupRef.setshowSequenceLogo(cprofl.getState());
+ aaa.groupRef.setshowSequenceLogo(cprofl.getState());
ap.repaint();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- ann.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
// automatically enable logo display if we're clicked
- ann.groupRef.setshowSequenceLogo(true);
+ aaa.groupRef.setshowSequenceLogo(true);
ap.repaint();
}
});
*/
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
MessageManager.getString("label.show_histogram"),
- av.isShowConsensusHistogram());
+ ap.av.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- av.setShowConsensusHistogram(chist.getState());
+ ap.av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.setMenusForViewport();
ap.repaint();
}
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
MessageManager.getString("label.show_logo"),
- av.isShowSequenceLogo());
+ ap.av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- av.setShowSequenceLogo(cprof.getState());
+ ap.av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.setMenusForViewport();
ap.repaint();
}
});
pop.add(cprof);
final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
MessageManager.getString("label.normalise_logo"),
- av.isNormaliseSequenceLogo());
+ ap.av.isNormaliseSequenceLogo());
cprofnorm.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- av.setShowSequenceLogo(true);
- av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.av.setShowSequenceLogo(true);
+ ap.av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.alignFrame.setMenusForViewport();
ap.repaint();
}
});
pop.add(cprofnorm);
}
- final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
- consclipbrd.addActionListener(this);
- pop.add(consclipbrd);
}
/**
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);
+ String msg = getStatusMessage(aa, anns);
+ ap.alignFrame.setStatus(msg);
+ }
+ }
- StringBuffer desc = new StringBuffer();
- if (aa.description != null
- && !aa.description.equals("New description"))
+ /**
+ * 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--)
{
- // TODO: we could refactor and merge this code with the code in
- // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
- // tooltips
- desc.append(aa.getDescription(true).trim());
- // check to see if the description is an html fragment.
- if (desc.length() < 6 || (desc.substring(0, 6).toLowerCase()
- .indexOf("<html>") < 0))
- {
- // clean the description ready for embedding in html
- desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
- .replaceAll("<"));
- desc.insert(0, "<html>");
- }
- else
+ if (anns[i].graphGroup == aa.graphGroup)
{
- // remove terminating html if any
- int i = desc.substring(desc.length() - 7).toLowerCase()
- .lastIndexOf("</html>");
- if (i > -1)
+ if (!first)
{
- desc.setLength(desc.length() - 7 + i);
+ msg.append(", ");
}
+ msg.append(anns[i].label);
+ first = false;
}
- if (aa.hasScore())
- {
- desc.append("<br/>");
- }
- // if (aa.hasProperties())
- // {
- // desc.append("<table>");
- // for (String prop : aa.getProperties())
- // {
- // desc.append("<tr><td>" + prop + "</td><td>"
- // + aa.getProperty(prop) + "</td><tr>");
- // }
- // desc.append("</table>");
- // }
- }
- else
- {
- // begin the tooltip's html fragment
- desc.append("<html>");
}
+ }
+
+ return msg.toString();
+ }
- if (aa.hasScore())
+ /**
+ * 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
+ * nor score is found.
+ *
+ * @param aa
+ * @return
+ */
+ static String getTooltip(AlignmentAnnotation aa)
+ {
+ if (aa == null)
+ {
+ return null;
+ }
+ StringBuilder tooltip = new StringBuilder();
+ if (aa.description != null && !aa.description.equals("New description"))
+ {
+ // TODO: we could refactor and merge this code with the code in
+ // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
+ // tooltips
+ String desc = aa.getDescription(true).trim();
+ if (!desc.toLowerCase().startsWith(HTML_START_TAG))
{
- // TODO: limit precision of score to avoid noise from imprecise
- // doubles
- // (64.7 becomes 64.7+/some tiny value).
- desc.append(" Score: " + aa.score);
+ tooltip.append(HTML_START_TAG);
+ desc = desc.replace("<", "<");
}
-
- if (desc.length() > 6)
+ else if (desc.toLowerCase().endsWith(HTML_END_TAG))
{
- desc.append("</html>");
- this.setToolTipText(desc.toString());
+ desc = desc.substring(0, desc.length() - HTML_END_TAG.length());
}
- else
+ tooltip.append(desc);
+ }
+ else
+ {
+ // begin the tooltip's html fragment
+ tooltip.append(HTML_START_TAG);
+ }
+ if (aa.hasScore())
+ {
+ if (tooltip.length() > HTML_START_TAG.length())
{
- this.setToolTipText(null);
+ tooltip.append("<br/>");
}
+ // TODO: limit precision of score to avoid noise from imprecise
+ // doubles
+ // (64.7 becomes 64.7+/some tiny value).
+ tooltip.append(" Score: ").append(String.valueOf(aa.score));
}
+
+ if (tooltip.length() > HTML_START_TAG.length())
+ {
+ return tooltip.append(HTML_END_TAG).toString();
+ }
+
+ /*
+ * nothing in the tooltip (except "<html>")
+ */
+ return null;
}
/**
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();
}
seqs, omitHidden, alignmentStartEnd);
Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(new StringSelection(output), Desktop.instance);
+ .setContents(new StringSelection(output), Desktop.getInstance());
HiddenColumns hiddenColumns = null;
av.getAlignment().getHiddenColumns());
}
- Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
- // of a consensus
- // sequence ? need to
- // flag
- // sequence as special.
+ // what is the dataset of a consensus sequence?
+ // need to flag sequence as special.
+ Desktop.getInstance().jalviewClipboard = new Object[] { seqs, ds,
hiddenColumns };
}
- /**
- * DOCUMENT ME!
- *
- * @param g1
- * DOCUMENT ME!
- */
@Override
public void paintComponent(Graphics g)
{
int width = getWidth();
if (width == 0)
{
- width = ap.calculateIdWidth().width + 4;
+ width = ap.calculateIdWidth().width;
}
Graphics2D g2 = (Graphics2D) g;
git://source.jalview.org / jalview.git / blobdiff