X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=85a2fbe1a3cd55b4ffef0ef498a3240470ba3571;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=62ed93c7e872e245ac56238e55ee77673da9a2d6;hpb=3971af0ab85bfd7a999415893c505eeae037b98e;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index 62ed93c..85a2fbe 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -1,28 +1,32 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; import java.util.*; - import java.awt.*; import java.awt.event.*; import jalview.datamodel.*; +import jalview.util.MessageManager; +import jalview.util.ParseHtmlBodyAndLinks; public class AnnotationLabels extends Panel implements ActionListener, MouseListener, MouseMotionListener @@ -57,11 +61,30 @@ public class AnnotationLabels extends Panel implements ActionListener, Tooltip tooltip; + private boolean hasHiddenRows; + public AnnotationLabels(AlignmentPanel ap) { 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); } @@ -71,30 +94,39 @@ public class AnnotationLabels extends Panel implements ActionListener, this.av = av; } - public void setScrollOffset(int y) + public void setScrollOffset(int y, boolean repaint) { scrollOffset = y; - repaint(); + if (repaint) + { + repaint(); + } } + /** + * + * @param y + * @return -2 if no rows are visible at all, -1 if no visible rows were + * selected + */ int getSelectedRow(int y) { - int row = -1; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + int row = -2; + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); if (aa == null) { return row; } - int height = 0; for (int i = 0; i < aa.length; i++) { + row = -1; if (!aa[i].visible) { continue; } - height += aa[i].height; if (y < height) { @@ -108,20 +140,20 @@ public class AnnotationLabels extends Panel implements ActionListener, public void actionPerformed(ActionEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (evt.getActionCommand().equals(ADDNEW)) { AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null, - new Annotation[ap.av.alignment.getWidth()]); + new Annotation[ap.av.getAlignment().getWidth()]); if (!editLabelDescription(newAnnotation)) { return; } - ap.av.alignment.addAnnotation(newAnnotation); - ap.av.alignment.setAnnotationIndex(newAnnotation, 0); + ap.av.getAlignment().addAnnotation(newAnnotation); + ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0); } else if (evt.getActionCommand().equals(EDITNAME)) { @@ -193,32 +225,110 @@ public class AnnotationLabels extends Panel implements ActionListener, } + boolean resizePanel = false; + public void mouseMoved(MouseEvent evt) { - int row = getSelectedRow(evt.getY() - scrollOffset); + resizePanel = evt.getY() < 10 && evt.getX() < 14; + int row = getSelectedRow(evt.getY() + scrollOffset); if (row > -1) { + ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks( + av.getAlignment().getAlignmentAnnotation()[row] + .getDescription(true), + true, "\n"); if (tooltip == null) { - tooltip = new Tooltip(ap.av.alignment.getAlignmentAnnotation()[row] - .getDescription(true), this); + tooltip = new Tooltip(phb.getNonHtmlContent(), this); } else { - tooltip.setTip(ap.av.alignment.getAlignmentAnnotation()[row] - .getDescription(true)); + tooltip.setTip(phb.getNonHtmlContent()); } } else if (tooltip != null) { tooltip.setTip(""); } + } + /** + * curent drag position + */ + MouseEvent dragEvent = null; + + /** + * flag to indicate drag events should be ignored + */ + private boolean dragCancelled = false; + + /** + * clear any drag events in progress + */ + public void cancelDrag() + { + dragEvent = null; + dragCancelled = true; } public void mouseDragged(MouseEvent evt) { + if (dragCancelled) + { + return; + } + ; + dragEvent = evt; + + if (resizePanel) + { + Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder + .getSize(), f = ap.seqPanelHolder.getSize(); + int dif = evt.getY() - oldY; + + dif /= ap.av.charHeight; + dif *= ap.av.charHeight; + + if ((d.height - dif) > 20 && (f.height + dif) > 20) + { + 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.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0, + av.calcPanelHeight()); + f.height += dif; + ap.seqPanelHolder.setPreferredSize(f); + ap.setScrollValues(av.getStartRes(), av.getStartSeq()); + ap.validate(); + // ap.paintAlignment(true); + ap.addNotify(); + } + + } + else + { + int diff; + if ((diff = 6 - evt.getY()) > 0) + { + // nudge scroll up + ap.apvscroll.setValue(ap.apvscroll.getValue() - diff); + ap.adjustmentValueChanged(null); + + } + else if ((0 < (diff = 6 + - ap.annotationSpaceFillerHolder.getSize().height + + evt.getY()))) + { + // nudge scroll down + ap.apvscroll.setValue(ap.apvscroll.getValue() + diff); + ap.adjustmentValueChanged(null); + } + repaint(); + } } public void mouseClicked(MouseEvent evt) @@ -227,70 +337,361 @@ public class AnnotationLabels extends Panel implements ActionListener, public void mouseReleased(MouseEvent evt) { + if (!resizePanel && !dragCancelled) + { + int start = selectedRow; + + int end = getSelectedRow(evt.getY() + scrollOffset); + + if (start > -1 && start != end) + { + // Swap these annotations + AlignmentAnnotation startAA = ap.av.getAlignment() + .getAlignmentAnnotation()[start]; + if (end == -1) + { + end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; + } + AlignmentAnnotation endAA = ap.av.getAlignment() + .getAlignmentAnnotation()[end]; + + ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; + ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; + } + } + resizePanel = false; + dragEvent = null; + dragCancelled = false; + repaint(); + ap.annotationPanel.repaint(); } public void mouseEntered(MouseEvent evt) { + if (evt.getY() < 10 && evt.getX() < 14) + { + resizePanel = true; + repaint(); + } } public void mouseExited(MouseEvent evt) { + dragCancelled = false; + + if (dragEvent == null) + { + resizePanel = false; + } + else + { + if (!resizePanel) + { + dragEvent = null; + } + } + repaint(); } public void mousePressed(MouseEvent evt) { - selectedRow = getSelectedRow(evt.getY() - scrollOffset); - - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - - PopupMenu popup = new PopupMenu("Annotations"); - - MenuItem item = new MenuItem(ADDNEW); - item.addActionListener(this); - popup.add(item); - if (aa == null) + oldY = evt.getY(); + if (resizePanel) { - - popup.show(this, evt.getX(), evt.getY()); return; } - // add the rest if there are actually rows to show - item = new MenuItem(EDITNAME); - item.addActionListener(this); - popup.add(item); - item = new MenuItem(HIDE); - item.addActionListener(this); - popup.add(item); - item = new MenuItem(SHOWALL); - item.addActionListener(this); - popup.add(item); - this.add(popup); - item = new MenuItem(OUTPUT_TEXT); - item.addActionListener(this); - popup.add(item); - - if (aa[selectedRow] == ap.av.consensus) + dragCancelled = false; + // todo: move below to mouseClicked ? + selectedRow = getSelectedRow(evt.getY() + scrollOffset); + + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + + // DETECT RIGHT MOUSE BUTTON IN AWT + if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) { - popup.addSeparator(); - final CheckboxMenuItem cbmi = new CheckboxMenuItem( - "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus()); - cbmi.addItemListener(new ItemListener() + PopupMenu popup = new PopupMenu( + MessageManager.getString("label.annotations")); + + MenuItem item = new MenuItem(ADDNEW); + item.addActionListener(this); + popup.add(item); + if (selectedRow < 0) { - public void itemStateChanged(ItemEvent e) + // this never happens at moment: - see comment on JAL-563 + if (hasHiddenRows) { - ap.av.setIgnoreGapsConsensus(cbmi.getState()); - ap.paintAlignment(true); + item = new MenuItem(SHOWALL); + item.addActionListener(this); + popup.add(item); } - }); - popup.add(cbmi); - item = new MenuItem(COPYCONS_SEQ); + this.add(popup); + popup.show(this, evt.getX(), evt.getY()); + return; + } + // add the rest if there are actually rows to show + item = new MenuItem(EDITNAME); item.addActionListener(this); popup.add(item); + item = new MenuItem(HIDE); + item.addActionListener(this); + popup.add(item); + if (hasHiddenRows) + { + item = new MenuItem(SHOWALL); + item.addActionListener(this); + popup.add(item); + } + this.add(popup); + item = new MenuItem(OUTPUT_TEXT); + item.addActionListener(this); + popup.add(item); + if (selectedRow < aa.length) + { + if (aa[selectedRow].autoCalculated) + { + if (aa[selectedRow].label.indexOf("Consensus") > -1) + { + popup.addSeparator(); + final CheckboxMenuItem cbmi = new CheckboxMenuItem( + MessageManager.getString("label.ignore_gaps_consensus"), + (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef + .getIgnoreGapsConsensus() : ap.av + .getIgnoreGapsConsensus()); + final AlignmentAnnotation aaa = aa[selectedRow]; + cbmi.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + if (aaa.groupRef != null) + { + // TODO: pass on reference to ap so the view can be updated. + aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); + } + else + { + ap.av.setIgnoreGapsConsensus(cbmi.getState()); + } + ap.paintAlignment(true); + } + }); + popup.add(cbmi); + if (aaa.groupRef != null) + { + final CheckboxMenuItem chist = new CheckboxMenuItem( + MessageManager.getString("label.show_group_histogram"), + aa[selectedRow].groupRef.isShowConsensusHistogram()); + chist.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setShowConsensusHistogram(chist.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + popup.add(chist); + final CheckboxMenuItem cprofl = new CheckboxMenuItem( + MessageManager.getString("label.show_group_logo"), + aa[selectedRow].groupRef.isShowSequenceLogo()); + cprofl.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setshowSequenceLogo(cprofl.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + + popup.add(cprofl); + final CheckboxMenuItem cprofn = new CheckboxMenuItem( + MessageManager.getString("label.normalise_group_logo"), + aa[selectedRow].groupRef.isNormaliseSequenceLogo()); + cprofn.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setshowSequenceLogo(true); + aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + popup.add(cprofn); + } + else + { + final CheckboxMenuItem chist = new CheckboxMenuItem( + MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram()); + chist.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowConsensusHistogram(chist.getState()); + ap.alignFrame.showConsensusHistogram.setState(chist + .getState()); // TODO: implement + // ap.updateGUI()/alignFrame.updateGUI + // for applet + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + popup.add(chist); + final CheckboxMenuItem cprof = new CheckboxMenuItem( + MessageManager.getString("label.show_logo"), av.isShowSequenceLogo()); + cprof.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowSequenceLogo(cprof.getState()); + ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO: + // implement + // ap.updateGUI()/alignFrame.updateGUI + // for + // applet + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + popup.add(cprof); + final CheckboxMenuItem cprofn = new CheckboxMenuItem( + MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo()); + cprofn.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowSequenceLogo(true); + 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()); + } + }); + popup.add(cprofn); + } + + item = new MenuItem(COPYCONS_SEQ); + item.addActionListener(this); + popup.add(item); + } + } + } + popup.show(this, evt.getX(), evt.getY()); } + else + { + // selection action. + if (selectedRow > -1 && selectedRow < aa.length) + { + if (aa[selectedRow].groupRef != null) + { + if (evt.getClickCount() >= 2) + { + // todo: make the ap scroll to the selection - not necessary, first + // click highlights/scrolls, second selects + ap.seqPanel.ap.idPanel.highlightSearchResults(null); + ap.av.setSelectionGroup(// new SequenceGroup( + aa[selectedRow].groupRef); // ); + ap.av.sendSelection(); + ap.paintAlignment(false); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + } + else + { + ap.seqPanel.ap.idPanel + .highlightSearchResults(aa[selectedRow].groupRef + .getSequences(null)); + } + return; + } + else if (aa[selectedRow].sequenceRef != null) + { + if (evt.getClickCount() == 1) + { + ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays + .asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); + } + else if (evt.getClickCount() >= 2) + { + ap.seqPanel.ap.idPanel.highlightSearchResults(null); + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg!=null) + { + // we make a copy rather than edit the current selection if no modifiers pressed + // see Enhancement JAL-1557 + if (!(evt.isControlDown() || evt.isShiftDown())) + { + sg = new SequenceGroup(sg); + sg.clear(); + sg.addSequence(aa[selectedRow].sequenceRef, false); + } else { + if (evt.isControlDown()) + { + sg.addOrRemove(aa[selectedRow].sequenceRef, true); + } else { + // notionally, we should also add intermediate sequences from last added sequence ? + sg.addSequence(aa[selectedRow].sequenceRef, true); + } + } + } else { + sg = new SequenceGroup(); + sg.setStartRes(0); + sg.setEndRes(ap.av.getAlignment().getWidth()-1); + sg.addSequence(aa[selectedRow].sequenceRef, false); + } + ap.av.setSelectionGroup(sg); + ap.paintAlignment(false); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); + } - popup.show(this, evt.getX(), evt.getY()); + } + } + } } /** @@ -309,7 +710,7 @@ public class AnnotationLabels extends Panel implements ActionListener, jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd() + "\t" + sq.getSequenceAsString() + "\n"); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector(); for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++) @@ -332,7 +733,9 @@ public class AnnotationLabels extends Panel implements ActionListener, public void paint(Graphics g) { int w = getSize().width; - if (image == null || w != image.getWidth(this)) + int h = getSize().height; + if (image == null || w != image.getWidth(this) + || h != image.getHeight(this)) { image = createImage(w, ap.annotationPanel.getSize().height); } @@ -348,41 +751,53 @@ public class AnnotationLabels extends Panel implements ActionListener, g.setColor(Color.white); g.fillRect(0, 0, getSize().width, getSize().height); - g.translate(0, scrollOffset); + g.translate(0, -scrollOffset); g.setColor(Color.black); - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int y = g.getFont().getSize(); - int x = 0; + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); + int y = 0, fy = g.getFont().getSize(); + int x = 0, offset; if (aa != null) { + hasHiddenRows = false; for (int i = 0; i < aa.length; i++) { if (!aa[i].visible) { + hasHiddenRows = true; continue; } x = width - fm.stringWidth(aa[i].label) - 3; - if (aa[i].graph > 0) - { - y += (aa[i].height / 3); - } - - g.drawString(aa[i].label, x, y); + y += aa[i].height; + offset = -(aa[i].height - fy) / 2; - if (aa[i].graph > 0) - { - y += (2 * aa[i].height / 3); - } - else - { - y += aa[i].height; - } + g.drawString(aa[i].label, x, y + offset); } } - } + 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) + { + g.setColor(Color.lightGray); + g.drawString(aa[selectedRow].label, dragEvent.getX(), + dragEvent.getY()); + } + if (!av.wrapAlignment && ((aa == null) || (aa.length < 1))) + { + g.setColor(Color.black); + g.drawString(MessageManager.getString("label.right_click"), 2, 8); + g.drawString(MessageManager.getString("label.to_add_annotation"), 2, + 18); + } + } }