X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=07c3e0af34527769886e942e9adf08384d1c4e9b;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=3f7e523548e2b74f190dac6e3be37ed9e42007ce;hpb=29c0f412ffb98c0b6d3d27714f2b6b032253f3bc;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index 3f7e523..07c3e0a 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -23,6 +23,7 @@ package jalview.appletgui; import jalview.analysis.AlignmentUtils; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.util.MessageManager; @@ -31,6 +32,7 @@ import jalview.util.ParseHtmlBodyAndLinks; import java.awt.Checkbox; import java.awt.CheckboxMenuItem; import java.awt.Color; +import java.awt.Cursor; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.FontMetrics; @@ -50,13 +52,22 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.util.Arrays; import java.util.Collections; -import java.util.Vector; -public class AnnotationLabels extends Panel implements ActionListener, - MouseListener, MouseMotionListener +public class AnnotationLabels extends Panel + implements ActionListener, MouseListener, MouseMotionListener { Image image; + /** + * width in pixels within which height adjuster arrows are shown and active + */ + private static final int HEIGHT_ADJUSTER_WIDTH = 50; + + /** + * height in pixels for allowing height adjuster to be active + */ + private static int HEIGHT_ADJUSTER_HEIGHT = 10; + boolean active = false; AlignmentPanel ap; @@ -92,23 +103,6 @@ public class AnnotationLabels extends Panel implements ActionListener, this.ap = ap; this.av = ap.av; setLayout(null); - - /** - * this retrieves the adjustable height glyph from resources. we don't use - * it at the moment. java.net.URL url = - * getClass().getResource("/images/idwidth.gif"); Image temp = null; - * - * if (url != null) { temp = - * java.awt.Toolkit.getDefaultToolkit().createImage(url); } - * - * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0); - * mt.waitForID(0); } catch (Exception ex) { } - * - * BufferedImage bi = new BufferedImage(temp.getHeight(this), - * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g = - * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90)); - * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi; - */ addMouseListener(this); addMouseMotionListener(this); } @@ -201,13 +195,16 @@ public class AnnotationLabels extends Panel implements ActionListener, ap.alignFrame); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle() - + " - " + aa[selectedRow].label, 500, 100); + jalview.bin.JalviewLite.addFrame(frame, + ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500, + 100); cap.setText(aa[selectedRow].toString()); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { - SequenceI cons = av.getConsensusSeq(); + SequenceGroup group = aa[selectedRow].groupRef; + SequenceI cons = group == null ? av.getConsensusSeq() + : group.getConsensusSeq(); if (cons != null) { copy_annotseqtoclipboard(cons); @@ -225,13 +222,15 @@ public class AnnotationLabels extends Panel implements ActionListener, ap.annotationPanel.adjustPanelHeight(); setSize(getSize().width, ap.annotationPanel.getSize().height); ap.validate(); - ap.paintAlignment(true); + // TODO: only paint if we needed to + ap.paintAlignment(true, true); } boolean editLabelDescription(AlignmentAnnotation annotation) { - Checkbox padGaps = new Checkbox("Fill Empty Gaps With \"" - + ap.av.getGapCharacter() + "\"", annotation.padGaps); + Checkbox padGaps = new Checkbox( + "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"", + annotation.padGaps); EditNameDialog dialog = new EditNameDialog(annotation.label, annotation.description, " Annotation Label", @@ -265,7 +264,10 @@ public class AnnotationLabels extends Panel implements ActionListener, @Override public void mouseMoved(MouseEvent evt) { - resizePanel = evt.getY() < 10 && evt.getX() < 14; + resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT + && evt.getX() < HEIGHT_ADJUSTER_WIDTH; + setCursor(Cursor.getPredefinedCursor( + resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR)); int row = getSelectedRow(evt.getY() + scrollOffset); if (row > -1) @@ -320,8 +322,9 @@ public class AnnotationLabels extends Panel implements ActionListener, if (resizePanel) { - Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder - .getSize(), f = ap.seqPanelHolder.getSize(); + Dimension d = ap.annotationPanelHolder.getSize(), + e = ap.annotationSpaceFillerHolder.getSize(), + f = ap.seqPanelHolder.getSize(); int dif = evt.getY() - oldY; dif /= ap.av.getCharHeight(); @@ -331,16 +334,16 @@ public class AnnotationLabels extends Panel implements ActionListener, { ap.annotationPanel.setSize(d.width, d.height - dif); setSize(new Dimension(e.width, d.height - dif)); - ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width, - d.height - dif)); - ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height - - dif)); + ap.annotationSpaceFillerHolder + .setSize(new Dimension(e.width, d.height - dif)); + ap.annotationPanelHolder + .setSize(new Dimension(d.width, d.height - dif)); ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0, av.calcPanelHeight()); f.height += dif; ap.seqPanelHolder.setPreferredSize(f); - ap.setScrollValues(av.getRanges().getStartRes(), av.getRanges() - .getStartSeq()); + ap.setScrollValues(av.getRanges().getStartRes(), + av.getRanges().getStartSeq()); ap.validate(); // ap.paintAlignment(true); ap.addNotify(); @@ -402,6 +405,7 @@ public class AnnotationLabels extends Panel implements ActionListener, resizePanel = false; dragEvent = null; dragCancelled = false; + setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); repaint(); ap.annotationPanel.repaint(); } @@ -414,6 +418,8 @@ public class AnnotationLabels extends Panel implements ActionListener, resizePanel = true; repaint(); } + setCursor(Cursor.getPredefinedCursor( + resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR)); } @Override @@ -451,7 +457,8 @@ public class AnnotationLabels extends Panel implements ActionListener, .getAlignmentAnnotation(); // DETECT RIGHT MOUSE BUTTON IN AWT - if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) + if ((evt.getModifiersEx() + & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK) { PopupMenu popup = new PopupMenu( @@ -525,9 +532,10 @@ public class AnnotationLabels extends Panel implements ActionListener, popup.addSeparator(); final CheckboxMenuItem cbmi = new CheckboxMenuItem( MessageManager.getString("label.ignore_gaps_consensus"), - (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef - .getIgnoreGapsConsensus() : ap.av - .isIgnoreGapsConsensus()); + (aa[selectedRow].groupRef != null) + ? aa[selectedRow].groupRef + .isIgnoreGapsConsensus() + : ap.av.isIgnoreGapsConsensus()); final AlignmentAnnotation aaa = aa[selectedRow]; cbmi.addItemListener(new ItemListener() { @@ -543,7 +551,7 @@ public class AnnotationLabels extends Panel implements ActionListener, { ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); } - ap.paintAlignment(true); + ap.paintAlignment(true, true); } }); popup.add(cbmi); @@ -631,10 +639,10 @@ public class AnnotationLabels extends Panel implements ActionListener, // can be // updated. av.setShowConsensusHistogram(chist.getState()); - ap.alignFrame.showConsensusHistogram.setState(chist - .getState()); // TODO: implement - // ap.updateGUI()/alignFrame.updateGUI - // for applet + ap.alignFrame.showConsensusHistogram + .setState(chist.getState()); // TODO: implement + // ap.updateGUI()/alignFrame.updateGUI + // for applet ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } @@ -680,11 +688,12 @@ public class AnnotationLabels extends Panel implements ActionListener, // can be // updated. av.setShowSequenceLogo(true); - ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO: - // implement - // ap.updateGUI()/alignFrame.updateGUI - // for - // applet + ap.alignFrame.normSequenceLogo + .setState(cprofn.getState()); // TODO: + // implement + // ap.updateGUI()/alignFrame.updateGUI + // for + // applet av.setNormaliseSequenceLogo(cprofn.getState()); ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); @@ -715,17 +724,16 @@ public class AnnotationLabels extends Panel implements ActionListener, ap.seqPanel.ap.idPanel.highlightSearchResults(null); // process modifiers SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg == null - || sg == aa[selectedRow].groupRef - || !(jalview.util.Platform.isControlDown(evt) || evt - .isShiftDown())) + if (sg == null || sg == aa[selectedRow].groupRef + || !(jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown())) { if (jalview.util.Platform.isControlDown(evt) || evt.isShiftDown()) { // clone a new selection group from the associated group - ap.av.setSelectionGroup(new SequenceGroup( - aa[selectedRow].groupRef)); + ap.av.setSelectionGroup( + new SequenceGroup(aa[selectedRow].groupRef)); } else { @@ -751,15 +759,14 @@ public class AnnotationLabels extends Panel implements ActionListener, } } } - ap.paintAlignment(false); + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } else { - ap.seqPanel.ap.idPanel - .highlightSearchResults(aa[selectedRow].groupRef - .getSequences(null)); + ap.seqPanel.ap.idPanel.highlightSearchResults( + aa[selectedRow].groupRef.getSequences(null)); } return; } @@ -768,8 +775,8 @@ public class AnnotationLabels extends Panel implements ActionListener, if (evt.getClickCount() == 1) { ap.seqPanel.ap.idPanel - .highlightSearchResults(Arrays - .asList(new SequenceI[] { aa[selectedRow].sequenceRef })); + .highlightSearchResults(Arrays.asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { @@ -780,8 +787,8 @@ public class AnnotationLabels extends Panel implements ActionListener, // we make a copy rather than edit the current selection if no // modifiers pressed // see Enhancement JAL-1557 - if (!(jalview.util.Platform.isControlDown(evt) || evt - .isShiftDown())) + if (!(jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown())) { sg = new SequenceGroup(sg); sg.clear(); @@ -809,7 +816,7 @@ public class AnnotationLabels extends Panel implements ActionListener, sg.addSequence(aa[selectedRow].sequenceRef, false); } ap.av.setSelectionGroup(sg); - ap.paintAlignment(false); + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } @@ -833,14 +840,13 @@ public class AnnotationLabels extends Panel implements ActionListener, return; } jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer(); - jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" - + sq.getStart() + "\t" + sq.getEnd() + "\t" - + sq.getSequenceAsString() + "\n"); + jalview.appletgui.AlignFrame.copiedSequences + .append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd() + + "\t" + sq.getSequenceAsString() + "\n"); if (av.hasHiddenColumns()) { - jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>( - av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy()); + jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns( + av.getAlignment().getHiddenColumns()); } } @@ -899,14 +905,8 @@ public class AnnotationLabels extends Panel implements ActionListener, } } g.translate(0, +scrollOffset); - if (resizePanel) - { - g.setColor(Color.red); - g.setPaintMode(); - g.drawLine(2, 8, 5, 2); - g.drawLine(5, 2, 8, 8); - } - else if (!dragCancelled && dragEvent != null && aa != null) + + if (!resizePanel && !dragCancelled && dragEvent != null && aa != null) { g.setColor(Color.lightGray); g.drawString(aa[selectedRow].label, dragEvent.getX(),