X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=52a6066db16bd0b27de610615574664aa6938374;hb=6003c80f7fe8bd5d1b8287e9e7126514b0d7e292;hp=9976604510dc300563812202b05c64ae553cd668;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 9976604..52a6066 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -20,23 +20,6 @@ */ package jalview.gui; -import java.util.Locale; - -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; @@ -53,9 +36,11 @@ import java.awt.event.MouseEvent; 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 javax.swing.JCheckBoxMenuItem; import javax.swing.JMenuItem; @@ -64,6 +49,26 @@ import javax.swing.JPopupMenu; 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.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.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 @@ -293,25 +298,21 @@ public class AnnotationLabels extends JPanel EditNameDialog dialog = new EditNameDialog(annotation.label, annotation.description, name, description); - dialog.showDialog(ap.alignFrame, title, new Runnable() - { - @Override - public void run() + dialog.showDialog(ap.alignFrame, title, () -> { + annotation.label = dialog.getName(); + String text = dialog.getDescription(); + if (text != null && text.length() == 0) { - 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); + text = null; } + annotation.description = text; + if (addNew) + { + ap.av.getAlignment().addAnnotation(annotation); + ap.av.getAlignment().setAnnotationIndex(annotation, 0); + } + ap.refresh(true); + return null; }); } @@ -421,6 +422,31 @@ public class AnnotationLabels extends JPanel consclipbrd.addActionListener(this); pop.add(consclipbrd); } + if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP + && PAEContactMatrix.PAEMATRIX + .equals(aa[selectedRow].getCalcId())) + { + final PAEContactMatrix cm = (PAEContactMatrix) av + .getContactMatrix(aa[selectedRow]); + if (cm!=null && cm.getNewick()!=null && cm.getNewick().length()>0) + { + item = new JMenuItem("Show Tree for Matrix"); + item.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + + ap.alignFrame.showContactMapTree(aa[selectedRow],cm); + + } + }); + pop.addSeparator(); + pop.add(item); + } + + } } pop.show(this, evt.getX(), evt.getY()); } @@ -1060,7 +1086,8 @@ public class AnnotationLabels extends JPanel 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; @@ -1085,6 +1112,7 @@ public class AnnotationLabels extends JPanel { hasHiddenRows = false; int olY = 0; + int nexAA = 0; for (int i = 0; i < aa.length; i++) { visible = true; @@ -1094,6 +1122,9 @@ public class AnnotationLabels extends JPanel continue; } olY = y; + // look ahead to next annotation + for (nexAA=i+1; nexAA -1) { @@ -1208,16 +1271,26 @@ public class AnnotationLabels extends JPanel } 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)))