X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=2786a08b8c800aaf2b2539dee85db0fb9be4890b;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=27c579a501786a997de783735a65086d024af8d6;hpb=78f929d85e95b6445f7fab46504abc394d8c3fe9;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index 27c579a..2786a08 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -1,19 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * 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. - * + * * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; @@ -21,9 +22,10 @@ import java.util.*; import java.awt.*; import java.awt.event.*; -import java.awt.image.BufferedImage; import jalview.datamodel.*; +import jalview.util.MessageManager; +import jalview.util.ParseHtmlBodyAndLinks; public class AnnotationLabels extends Panel implements ActionListener, MouseListener, MouseMotionListener @@ -91,10 +93,13 @@ 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(); + } } /** @@ -106,7 +111,8 @@ public class AnnotationLabels extends Panel implements ActionListener, int getSelectedRow(int y) { int row = -2; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); if (aa == null) { @@ -133,20 +139,20 @@ 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)) { @@ -227,17 +233,17 @@ public class AnnotationLabels extends Panel implements ActionListener, 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) @@ -292,7 +298,7 @@ public class AnnotationLabels extends Panel implements ActionListener, ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height - dif)); ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0, - ap.annotationPanel.calcPanelHeight()); + av.calcPanelHeight()); f.height += dif; ap.seqPanelHolder.setPreferredSize(f); ap.setScrollValues(av.getStartRes(), av.getStartSeq()); @@ -330,26 +336,26 @@ public class AnnotationLabels extends Panel implements ActionListener, public void mouseReleased(MouseEvent evt) { - if (!dragCancelled) + if (!resizePanel && !dragCancelled) { int start = selectedRow; int end = getSelectedRow(evt.getY() + scrollOffset); - if (start != end) + if (start > -1 && start != end) { // Swap these annotations - AlignmentAnnotation startAA = ap.av.alignment + AlignmentAnnotation startAA = ap.av.getAlignment() .getAlignmentAnnotation()[start]; if (end == -1) { - end = ap.av.alignment.getAlignmentAnnotation().length - 1; + end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; } - AlignmentAnnotation endAA = ap.av.alignment + AlignmentAnnotation endAA = ap.av.getAlignment() .getAlignmentAnnotation()[end]; - ap.av.alignment.getAlignmentAnnotation()[end] = startAA; - ap.av.alignment.getAlignmentAnnotation()[start] = endAA; + ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; + ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; } } resizePanel = false; @@ -393,17 +399,18 @@ public class AnnotationLabels extends Panel implements ActionListener, { return; } - dragCancelled=false; + dragCancelled = false; // todo: move below to mouseClicked ? selectedRow = getSelectedRow(evt.getY() + scrollOffset); - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); // DETECT RIGHT MOUSE BUTTON IN AWT if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) { - PopupMenu popup = new PopupMenu("Annotations"); + PopupMenu popup = new PopupMenu(MessageManager.getString("label.annotations")); MenuItem item = new MenuItem(ADDNEW); item.addActionListener(this); @@ -507,7 +514,28 @@ public class AnnotationLabels extends Panel implements ActionListener, // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } }); + popup.add(cprofl); + final CheckboxMenuItem cprofn = new CheckboxMenuItem( + "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 { @@ -524,6 +552,10 @@ 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.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } @@ -542,11 +574,40 @@ public class AnnotationLabels extends Panel implements ActionListener, // 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( + "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); @@ -624,7 +685,7 @@ 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++) @@ -647,7 +708,9 @@ 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); } @@ -666,7 +729,7 @@ public class AnnotationLabels extends Panel implements ActionListener, g.translate(0, -scrollOffset); g.setColor(Color.black); - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); int y = 0, fy = g.getFont().getSize(); int x = 0, offset; @@ -704,11 +767,11 @@ public class AnnotationLabels extends Panel implements ActionListener, dragEvent.getY()); } - if ((aa == null) || (aa.length < 1)) + if (!av.wrapAlignment && ((aa == null) || (aa.length < 1))) { g.setColor(Color.black); - g.drawString("Right click", 2, 8); - g.drawString("to add annotation", 2, 18); + g.drawString(MessageManager.getString("label.right_click"), 2, 8); + g.drawString(MessageManager.getString("label.to_add_annotation"), 2, 18); } } }