X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=c883071187b4d997ded9c22ad01fa9aecb064bf3;hb=405e8b16ccb9b1297e1158ace036f0b1634dac67;hp=1a9541c3794b0a2b44d34ca02bea69145b767270;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 1a9541c..c883071 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -24,9 +24,11 @@ import jalview.analysis.AlignmentUtils; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.io.FileFormat; import jalview.io.FormatAdapter; import jalview.util.MessageManager; @@ -48,10 +50,9 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; 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.List; +import java.util.Iterator; import java.util.regex.Pattern; import javax.swing.JCheckBoxMenuItem; @@ -67,8 +68,8 @@ import javax.swing.ToolTipManager; * @author $author$ * @version $Revision$ */ -public class AnnotationLabels extends JPanel implements MouseListener, - MouseMotionListener, ActionListener +public class AnnotationLabels extends JPanel + implements MouseListener, MouseMotionListener, ActionListener { private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern .compile("<"); @@ -267,7 +268,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, else if (evt.getActionCommand().equals(OUTPUT_TEXT)) { new AnnotationExporter().exportAnnotations(ap, - new AlignmentAnnotation[] { aa[selectedRow] }); + new AlignmentAnnotation[] + { aa[selectedRow] }); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { @@ -291,33 +293,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - refresh(fullRepaint); + ap.refresh(fullRepaint); } /** - * Redraw sensibly. - * - * @adjustHeight if true, try to recalculate panel height for visible - * annotations - */ - protected void refresh(boolean adjustHeight) - { - ap.validateAnnotationDimensions(adjustHeight); - ap.addNotify(); - if (adjustHeight) - { - // sort, repaint, update overview - ap.paintAlignment(true); - } - else - { - // lightweight repaint - ap.repaint(); - } - } - - /** * DOCUMENT ME! * * @param e @@ -419,7 +399,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, // ann.visible = false; // } // } - refresh(true); + ap.refresh(true); } }); pop.add(hideType); @@ -461,9 +441,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, // av and sequencegroup need to implement same interface for final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( MessageManager.getString("label.ignore_gaps_consensus"), - (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef - .getIgnoreGapsConsensus() : ap.av - .isIgnoreGapsConsensus()); + (aa[selectedRow].groupRef != null) + ? aa[selectedRow].groupRef.getIgnoreGapsConsensus() + : ap.av.isIgnoreGapsConsensus()); final AlignmentAnnotation aaa = aa[selectedRow]; cbmi.addActionListener(new ActionListener() { @@ -474,8 +454,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { // TODO: pass on reference to ap so the view can be updated. aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); - ap.getAnnotationPanel().paint( - ap.getAnnotationPanel().getGraphics()); + ap.getAnnotationPanel() + .paint(ap.getAnnotationPanel().getGraphics()); } else { @@ -721,12 +701,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, if ((d.height - dif) > 20) { - ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height - dif)); + ap.annotationScroller + .setPreferredSize(new Dimension(d.width, d.height - dif)); d = ap.annotationSpaceFillerHolder.getPreferredSize(); - ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( - d.width, d.height - dif)); - ap.paintAlignment(true); + ap.annotationSpaceFillerHolder + .setPreferredSize(new Dimension(d.width, d.height - dif)); + ap.paintAlignment(true, false); } ap.addNotify(); @@ -750,8 +730,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, getSelectedRow(evt.getY() - getScrollOffset()); - if (selectedRow > -1 - && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) + if (selectedRow > -1 && ap.av.getAlignment() + .getAlignmentAnnotation().length > selectedRow) { AlignmentAnnotation aa = ap.av.getAlignment() .getAlignmentAnnotation()[selectedRow]; @@ -765,8 +745,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, // 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(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc) @@ -840,17 +820,16 @@ public class AnnotationLabels extends JPanel implements MouseListener, ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); // process modifiers SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg == null - || sg == aa[selectedRow].groupRef - || !(jalview.util.Platform.isControlDown(evt) || evt - .isShiftDown())) + if (sg == null || sg == aa[selectedRow].groupRef + || !(jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown())) { if (jalview.util.Platform.isControlDown(evt) || evt.isShiftDown()) { // clone a new selection group from the associated group - ap.av.setSelectionGroup(new SequenceGroup( - aa[selectedRow].groupRef)); + ap.av.setSelectionGroup( + new SequenceGroup(aa[selectedRow].groupRef)); } else { @@ -877,7 +856,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } } - ap.paintAlignment(false); + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } @@ -892,10 +871,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() == 1) { - ap.getSeqPanel().ap - .getIdPanel() - .highlightSearchResults( - Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef })); + ap.getSeqPanel().ap.getIdPanel() + .highlightSearchResults(Arrays.asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { @@ -906,8 +884,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, // we make a copy rather than edit the current selection if no // modifiers pressed // see Enhancement JAL-1557 - if (!(jalview.util.Platform.isControlDown(evt) || evt - .isShiftDown())) + if (!(jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown())) { sg = new SequenceGroup(sg); sg.clear(); @@ -935,7 +913,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, sg.addSequence(aa[selectedRow].sequenceRef, false); } ap.av.setSelectionGroup(sg); - ap.paintAlignment(false); + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } @@ -968,31 +946,30 @@ public class AnnotationLabels extends JPanel implements MouseListener, Alignment ds = new Alignment(dseqs); if (av.hasHiddenColumns()) { - omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, - sq.getLength(), seqs); + Iterator it = av.getAlignment().getHiddenColumns() + .getVisContigsIterator(0, sq.getLength(), false); + omitHidden = new String[] { sq.getSequenceStringFromIterator(it) }; } int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; - List hiddenCols = av.getColumnSelection().getHiddenColumns(); - if (hiddenCols != null) + if (av.hasHiddenColumns()) { - alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex( - hiddenCols); + alignmentStartEnd = av.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(av.getAlignment().getWidth()); } - String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden, alignmentStartEnd); + + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, + seqs, omitHidden, alignmentStartEnd); Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(output), Desktop.instance); - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; + if (av.hasHiddenColumns()) { - hiddenColumns = new ArrayList(); - for (int[] region : av.getColumnSelection().getHiddenColumns()) - { - hiddenColumns.add(new int[] { region[0], region[1] }); - } + hiddenColumns = new HiddenColumns( + av.getAlignment().getHiddenColumns()); } Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset @@ -1088,8 +1065,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, int ofontH = fontHeight; int sOffset = 0; int visHeight = 0; - int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap - .getAnnotationPanel().getVisibleVRange() : null; + int[] visr = (ap != null && ap.getAnnotationPanel() != null) + ? ap.getAnnotationPanel().getVisibleVRange() + : null; if (clip && visr != null) { sOffset = visr[0]; @@ -1132,8 +1110,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (debugRedraw) { - System.out.println("Scroll offset: " + sOffset - + " after vis: " + i); + System.out.println( + "Scroll offset: " + sOffset + " after vis: " + i); } after = true; } @@ -1171,7 +1149,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, } if (groupSize * (fontHeight + 8) < aa[i].height) { - graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; } else { @@ -1185,11 +1164,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, { fontHeight = -8 + (int) h; s = ((float) fontHeight) / (float) ofontH; - Font f = baseFont.deriveFont(AffineTransform - .getScaleInstance(s, s)); + Font f = baseFont + .deriveFont(AffineTransform.getScaleInstance(s, s)); g.setFont(f); fm = g.getFontMetrics(); - graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; } } if (visible) @@ -1206,8 +1186,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.setColor(aa[gg]._linecolour); g.drawLine(x, y - graphExtras + 3, - x + fm.stringWidth(aa[gg].label), y - graphExtras - + 3); + x + fm.stringWidth(aa[gg].label), + y - graphExtras + 3); } g.setColor(Color.black);