X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=0378753a7e62a8a71e5bae708909eaf0197bc388;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=665537c55ed0ba860bc0a74a3f4b5f43e3d199ab;hpb=20947b2cc413aba4422bf03466c5f4a60c23bd9b;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 665537c..0378753 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,19 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.gui; @@ -29,6 +30,7 @@ import javax.swing.*; import jalview.datamodel.*; import jalview.io.*; +import jalview.util.MessageManager; /** * DOCUMENT ME! @@ -115,6 +117,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, addMouseListener(this); addMouseMotionListener(this); + addMouseWheelListener(ap.annotationPanel); } public AnnotationLabels(AlignViewport av) @@ -144,7 +147,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, void getSelectedRow(int y) { int height = 0; - AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); selectedRow = -2; if (aa != null) { @@ -176,7 +180,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void actionPerformed(ActionEvent evt) { - AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); if (evt.getActionCommand().equals(ADDNEW)) { @@ -245,8 +250,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, ap.validateAnnotationDimensions(false); ap.addNotify(); ap.repaint(); - //validate(); - //ap.paintAlignment(true); + // validate(); + // ap.paintAlignment(true); } /** @@ -312,7 +317,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; } - AlignmentAnnotation endAA = ap.av.getAlignment().getAlignmentAnnotation()[end]; + AlignmentAnnotation endAA = ap.av.getAlignment() + .getAlignmentAnnotation()[end]; ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; @@ -405,40 +411,51 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (selectedRow > -1 && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) { - AlignmentAnnotation aa = ap.av.getAlignment().getAlignmentAnnotation()[selectedRow]; - + AlignmentAnnotation aa = ap.av.getAlignment() + .getAlignmentAnnotation()[selectedRow]; + StringBuffer desc = new StringBuffer(); 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 + // 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("")<0)) + if (desc.length() < 6 + || (desc.substring(0, 6).toLowerCase().indexOf("") < 0)) { // clean the description ready for embedding in html - desc = new StringBuffer(Pattern.compile("<").matcher(desc).replaceAll("<")); + desc = new StringBuffer(Pattern.compile("<").matcher(desc) + .replaceAll("<")); desc.insert(0, ""); - } else { - // remove terminating html if any - int i=desc.substring(desc.length()-7).toLowerCase().lastIndexOf(""); - if (i>-1) { - desc.setLength(desc.length()-7+i); - } + } + else + { + // remove terminating html if any + int i = desc.substring(desc.length() - 7).toLowerCase() + .lastIndexOf(""); + if (i > -1) + { + desc.setLength(desc.length() - 7 + i); + } } if (aa.hasScore()) { desc.append("
"); } - - - } else { + + } + else + { // begin the tooltip's html fragment desc.append(""); } if (aa.hasScore()) { - // TODO: limit precision of score to avoid noise from imprecise doubles (64.7 becomes 64.7+/some tiny value). + // TODO: limit precision of score to avoid noise from imprecise doubles + // (64.7 becomes 64.7+/some tiny value). desc.append(" Score: " + aa.score); } @@ -461,7 +478,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void mouseClicked(MouseEvent evt) { - AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); if (SwingUtilities.isLeftMouseButton(evt)) { if (selectedRow > -1 && selectedRow < aa.length) @@ -470,7 +488,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() >= 2) { - // todo: make the ap scroll to the selection - not necessary, first click highlights/scrolls, second selects + // 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); // ); @@ -513,7 +532,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, return; } - JPopupMenu pop = new JPopupMenu("Annotations"); + JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.annotations")); JMenuItem item = new JMenuItem(ADDNEW); item.addActionListener(this); pop.add(item); @@ -638,7 +657,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, { public void actionPerformed(ActionEvent e) { - + // TODO: pass on reference // to ap // so the @@ -799,18 +818,32 @@ public class AnnotationLabels extends JPanel implements MouseListener, RenderingHints.VALUE_ANTIALIAS_ON); } - drawComponent(g2, width); + drawComponent(g2, true, width); } /** - * DOCUMENT ME! + * Draw the full set of annotation Labels for the alignment at the given cursor * - * @param g - * DOCUMENT ME! + * @param g Graphics2D instance (needed for font scaling) + * @param width Width for scaling labels + * */ public void drawComponent(Graphics g, int width) { + drawComponent(g, false, width); + } + + private final boolean debugRedraw = false; + /** + * Draw the full set of annotation Labels for the alignment at the given cursor + * + * @param g Graphics2D instance (needed for font scaling) + * @param clip - true indicates that only current visible area needs to be rendered + * @param width Width for scaling labels + */ + public void drawComponent(Graphics g, boolean clip, int width) + { if (av.getFont().getSize() < 10) { g.setFont(font); @@ -826,7 +859,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.translate(0, scrollOffset); g.setColor(Color.black); - + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); int fontHeight = g.getFont().getSize(); int y = 0; @@ -836,22 +869,54 @@ public class AnnotationLabels extends JPanel implements MouseListener, Font baseFont = g.getFont(); FontMetrics baseMetrics = fm; int ofontH = fontHeight; - boolean visible = true; + int sOffset=0; + int visHeight = 0; + int[] visr = (ap!=null && ap.annotationPanel!=null) ? ap.annotationPanel.getVisibleVRange() : null; + if (clip && visr!=null){ + sOffset = visr[0]; + visHeight = visr[1]; + } + boolean visible = true,before=false,after=false; if (aa != null) { hasHiddenRows = false; + int olY=0; for (int i = 0; i < aa.length; i++) { visible = true; - g.setColor(Color.black); - if (!aa[i].visible) { hasHiddenRows = true; continue; } - + olY=y; y += aa[i].height; + if (clip) {if (yvisHeight) + { + + if (!after) + { + if (debugRedraw) { + System.out.println("Scroll offset: "+sOffset+" after vis: "+i); + } + after=true; + } + // don't draw what isn't visible + continue; + }} + g.setColor(Color.black); offset = -aa[i].height / 2; @@ -868,6 +933,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (aa[i].graphGroup > -1) { int groupSize = 0; + // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels for (int gg = 0; gg < aa.length; gg++) { if (aa[gg].graphGroup == aa[i].graphGroup) @@ -906,7 +972,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, { x = width - fm.stringWidth(aa[gg].label) - 3; g.drawString(aa[gg].label, x, y - graphExtras); - + if (aa[gg]._linecolour != null) { @@ -943,10 +1009,10 @@ public class AnnotationLabels extends JPanel implements MouseListener, dragEvent.getY() - scrollOffset); } - if ((aa == null) || (aa.length < 1)) + if (!av.wrapAlignment && ((aa == null) || (aa.length < 1))) { - 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); } } }