X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=2178e37ef8abb920386662214a112048dc40761c;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=7967ae63cd2e4a34fdec448120ef0f67ee0ed049;hpb=bbfdb203ce3a889600caa52478478b75ab03809f;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 7967ae6..2178e37 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 2.8.1) + * 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; @@ -23,11 +24,13 @@ import java.util.regex.Pattern; import java.awt.*; import java.awt.datatransfer.*; import java.awt.event.*; +import java.awt.geom.AffineTransform; import java.awt.image.*; import javax.swing.*; import jalview.datamodel.*; import jalview.io.*; +import jalview.util.MessageManager; /** * DOCUMENT ME! @@ -114,6 +117,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, addMouseListener(this); addMouseMotionListener(this); + addMouseWheelListener(ap.annotationPanel); } public AnnotationLabels(AlignViewport av) @@ -143,7 +147,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, void getSelectedRow(int y) { int height = 0; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); selectedRow = -2; if (aa != null) { @@ -175,20 +180,21 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void actionPerformed(ActionEvent evt) { - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); if (evt.getActionCommand().equals(ADDNEW)) { AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, - null, new Annotation[ap.av.alignment.getWidth()]); + null, 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)) { @@ -201,7 +207,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else if (evt.getActionCommand().equals(DELETE)) { - ap.av.alignment.deleteAnnotation(aa[selectedRow]); + ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); } else if (evt.getActionCommand().equals(SHOWALL)) { @@ -244,8 +250,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, ap.validateAnnotationDimensions(false); ap.addNotify(); ap.repaint(); - //validate(); - //ap.paintAlignment(true); + // validate(); + // ap.paintAlignment(true); } /** @@ -305,16 +311,17 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (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.getAlignmentAnnotation()[end]; + 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; @@ -402,42 +409,53 @@ public class AnnotationLabels extends JPanel implements MouseListener, getSelectedRow(evt.getY() - scrollOffset); if (selectedRow > -1 - && ap.av.alignment.getAlignmentAnnotation().length > selectedRow) + && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) { - AlignmentAnnotation aa = ap.av.alignment.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); } @@ -460,7 +478,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void mouseClicked(MouseEvent evt) { - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); if (SwingUtilities.isLeftMouseButton(evt)) { if (selectedRow > -1 && selectedRow < aa.length) @@ -469,7 +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); // ); @@ -512,7 +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); @@ -637,7 +657,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, { public void actionPerformed(ActionEvent e) { - + // TODO: pass on reference // to ap // so the @@ -744,7 +764,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, sq.setDatasetSequence(dseqs[0]); } Alignment ds = new Alignment(dseqs); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs); @@ -757,7 +777,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, .setContents(new StringSelection(output), Desktop.instance); Vector hiddenColumns = null; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { hiddenColumns = new Vector(); for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++) @@ -798,18 +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); @@ -825,28 +859,64 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.translate(0, scrollOffset); g.setColor(Color.black); - - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); int fontHeight = g.getFont().getSize(); int y = 0; int x = 0; int graphExtras = 0; int offset = 0; - + Font baseFont = g.getFont(); + FontMetrics baseMetrics = fm; + int ofontH = fontHeight; + 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++) { - g.setColor(Color.black); - + visible = true; 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; @@ -863,6 +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) @@ -870,30 +941,55 @@ public class AnnotationLabels extends JPanel implements MouseListener, groupSize++; } } - if (groupSize * (fontHeight + 8) < aa[i].height) { graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; } - - for (int gg = 0; gg < aa.length; gg++) + else { - if (aa[gg].graphGroup == aa[i].graphGroup) + // scale font to fit + float h = aa[i].height / (float) groupSize, s; + if (h < 9) { - x = width - fm.stringWidth(aa[gg].label) - 3; - g.drawString(aa[gg].label, x, y - graphExtras); - if (aa[gg].annotations[0] != null) + visible = false; + } + else + { + fontHeight = -8 + (int) h; + s = ((float) fontHeight) / (float) ofontH; + Font f = baseFont.deriveFont(AffineTransform + .getScaleInstance(s, s)); + g.setFont(f); + fm = g.getFontMetrics(); + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + } + } + if (visible) + { + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == aa[i].graphGroup) { - g.setColor(aa[gg].annotations[0].colour); - } + x = width - fm.stringWidth(aa[gg].label) - 3; + g.drawString(aa[gg].label, x, y - graphExtras); + + if (aa[gg]._linecolour != null) + { - g.drawLine(x, y - graphExtras - 3, - x + fm.stringWidth(aa[gg].label), y - graphExtras - 3); + g.setColor(aa[gg]._linecolour); + g.drawLine(x, y - graphExtras + 3, + x + fm.stringWidth(aa[gg].label), y - graphExtras + + 3); + } - g.setColor(Color.black); - graphExtras += fontHeight + 8; + g.setColor(Color.black); + graphExtras += fontHeight + 8; + } } } + g.setFont(baseFont); + fm = baseMetrics; + fontHeight = ofontH; } else { @@ -913,10 +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); } } }