X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=a5448133ca9a0a24eb1b7c84c4e240d45f1755f2;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=9c357a0ee44c4f5816232091ef8e83c9fd3a6d6a;hpb=10e637daad8983c41db8679baabea5563d7371f4;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 9c357a0..a544813 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -20,15 +20,6 @@ */ package jalview.gui; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.Annotation; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.io.FormatAdapter; -import jalview.util.MessageManager; - import java.awt.Color; import java.awt.Dimension; import java.awt.Font; @@ -49,6 +40,7 @@ import java.awt.geom.AffineTransform; import java.awt.image.BufferedImage; import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; import java.util.regex.Pattern; import javax.swing.JCheckBoxMenuItem; @@ -58,6 +50,16 @@ import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; +import jalview.analysis.AlignmentUtils; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.FormatAdapter; +import jalview.util.MessageManager; + /** * DOCUMENT ME! * @@ -67,6 +69,8 @@ import javax.swing.ToolTipManager; public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { + private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<"); + String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column"); String ADDNEW = MessageManager.getString("label.add_new_row"); @@ -408,8 +412,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, Dimension d = ap.annotationScroller.getPreferredSize(); int dif = evt.getY() - oldY; - dif /= ap.av.charHeight; - dif *= ap.av.charHeight; + dif /= ap.av.getCharHeight(); + dif *= ap.av.getCharHeight(); if ((d.height - dif) > 20) { @@ -460,7 +464,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, || (desc.substring(0, 6).toLowerCase().indexOf("") < 0)) { // clean the description ready for embedding in html - desc = new StringBuffer(Pattern.compile("<").matcher(desc) + desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc) .replaceAll("<")); desc.insert(0, ""); } @@ -621,11 +625,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, item.addActionListener(this); pop.add(item); // JAL-1264 hide all sequence-specific annotations of this type - final String label = aa[selectedRow].label; if (selectedRow < aa.length) { if (aa[selectedRow].sequenceRef != null) { + final String label = aa[selectedRow].label; JMenuItem hideType = new JMenuItem(); String text = MessageManager.getString("label.hide_all") + " " + label; hideType.setText(text); @@ -634,15 +638,18 @@ public class AnnotationLabels extends JPanel implements MouseListener, @Override public void actionPerformed(ActionEvent e) { - for (AlignmentAnnotation ann : ap.av.getAlignment() - .getAlignmentAnnotation()) - { - if (ann.sequenceRef != null && ann.label != null - && ann.label.equals(label)) - { - ann.visible = false; - } - } + AlignmentUtils.showOrHideSequenceAnnotations( + ap.av.getAlignment(), Collections.singleton(label), + null, false, false); + // for (AlignmentAnnotation ann : ap.av.getAlignment() + // .getAlignmentAnnotation()) + // { + // if (ann.sequenceRef != null && ann.label != null + // && ann.label.equals(label)) + // { + // ann.visible = false; + // } + // } refresh(); } }); @@ -665,6 +672,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, // property methods if (selectedRow < aa.length) { + final String label = aa[selectedRow].label; if (!aa[selectedRow].autoCalculated) { if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) @@ -683,10 +691,10 @@ public class AnnotationLabels extends JPanel implements MouseListener, pop.addSeparator(); // av and sequencegroup need to implement same interface for final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - MessageManager.getString("label.ignore_gaps_consensus"), + MessageManager.getString("label.ignore_gaps_consensus"), (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef .getIgnoreGapsConsensus() : ap.av - .getIgnoreGapsConsensus()); + .isIgnoreGapsConsensus()); final AlignmentAnnotation aaa = aa[selectedRow]; cbmi.addActionListener(new ActionListener() { @@ -709,7 +717,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (aaa.groupRef != null) { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_histogram"), + MessageManager.getString("label.show_group_histogram"), aa[selectedRow].groupRef.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { @@ -728,7 +736,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_logo"), + MessageManager.getString("label.show_group_logo"), aa[selectedRow].groupRef.isShowSequenceLogo()); cprofl.addActionListener(new ActionListener() { @@ -747,7 +755,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprofl); final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_group_logo"), + MessageManager.getString("label.normalise_group_logo"), aa[selectedRow].groupRef.isNormaliseSequenceLogo()); cproflnorm.addActionListener(new ActionListener() { @@ -772,7 +780,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, else { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram()); + MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -791,7 +799,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - MessageManager.getString("label.show_logo"), av.isShowSequenceLogo()); + MessageManager.getString("label.show_logo"), av.isShowSequenceLogo()); cprof.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -810,7 +818,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprof); final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo()); + MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo()); cprofnorm.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1122,7 +1130,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, dragEvent.getY() - getScrollOffset()); } - if (!av.wrapAlignment && ((aa == null) || (aa.length < 1))) + if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1))) { g.drawString(MessageManager.getString("label.right_click"), 2, 8); g.drawString(MessageManager.getString("label.to_add_annotation"), 2,