X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=f732a36dc39fef6c4bb6acd638744cf79b092dae;hb=1718e104b60584336348531e51c8121d69ff6416;hp=ad6f9e509743e7db3e3374937d0da7c055488c28;hpb=defbcc5ef50f2287ea40d4a196495ba33b986eb7;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index ad6f9e5..f732a36 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -47,8 +47,8 @@ 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.Vector; import java.util.regex.Pattern; import javax.swing.JCheckBoxMenuItem; @@ -99,7 +99,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, int selectedRow; - int scrollOffset = 0; + private int scrollOffset = 0; Font font = new Font("Arial", Font.PLAIN, 11); @@ -143,7 +143,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, addMouseListener(this); addMouseMotionListener(this); - addMouseWheelListener(ap.annotationPanel); + addMouseWheelListener(ap.getAnnotationPanel()); } public AnnotationLabels(AlignViewport av) @@ -249,7 +249,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, { new AnnotationExporter().exportAnnotations(ap, new AlignmentAnnotation[] - { aa[selectedRow] }, null, null); + { aa[selectedRow] }); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { @@ -325,7 +325,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void mousePressed(MouseEvent evt) { - getSelectedRow(evt.getY() - scrollOffset); + getSelectedRow(evt.getY() - getScrollOffset()); oldY = evt.getY(); } @@ -338,7 +338,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, public void mouseReleased(MouseEvent evt) { int start = selectedRow; - getSelectedRow(evt.getY() - scrollOffset); + getSelectedRow(evt.getY() - getScrollOffset()); int end = selectedRow; if (start != end) @@ -360,7 +360,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, resizePanel = false; dragEvent = null; repaint(); - ap.annotationPanel.repaint(); + ap.getAnnotationPanel().repaint(); } /** @@ -439,7 +439,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, { resizePanel = evt.getY() < 10; - getSelectedRow(evt.getY() - scrollOffset); + getSelectedRow(evt.getY() - getScrollOffset()); if (selectedRow > -1 && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) @@ -478,20 +478,29 @@ public class AnnotationLabels extends JPanel implements MouseListener, { desc.append("
"); } - + // if (aa.hasProperties()) + // { + // desc.append(""); + // for (String prop : aa.getProperties()) + // { + // desc.append(""); + // } + // desc.append("
" + prop + "" + // + aa.getProperty(prop) + "
"); + // } } 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). + desc.append(" Score: " + aa.score); + } } - if (aa.hasScore()) - { - // TODO: limit precision of score to avoid noise from imprecise doubles - // (64.7 becomes 64.7+/some tiny value). - desc.append(" Score: " + aa.score); - } - if (desc.length() > 6) { desc.append(""); @@ -502,7 +511,6 @@ public class AnnotationLabels extends JPanel implements MouseListener, this.setToolTipText(null); } } - } /** @@ -525,7 +533,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, { // todo: make the ap scroll to the selection - not necessary, first // click highlights/scrolls, second selects - ap.seqPanel.ap.idPanel.highlightSearchResults(null); + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); ap.av.setSelectionGroup(// new SequenceGroup( aa[selectedRow].groupRef); // ); ap.paintAlignment(false); @@ -534,7 +542,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else { - ap.seqPanel.ap.idPanel + ap.getSeqPanel().ap.getIdPanel() .highlightSearchResults(aa[selectedRow].groupRef .getSequences(null)); } @@ -544,13 +552,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() == 1) { - ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(Arrays .asList(new SequenceI[] { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { - ap.seqPanel.ap.idPanel.highlightSearchResults(null); + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); SequenceGroup sg = ap.av.getSelectionGroup(); if (sg!=null) { @@ -688,7 +696,7 @@ 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.annotationPanel.paint(ap.annotationPanel.getGraphics()); + ap.getAnnotationPanel().paint(ap.getAnnotationPanel().getGraphics()); } else { @@ -864,16 +872,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(output), Desktop.instance); - Vector hiddenColumns = null; + ArrayList hiddenColumns = null; if (av.hasHiddenColumns()) { - hiddenColumns = new Vector(); - for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++) + hiddenColumns = new ArrayList(); + for (int[] region : av.getColumnSelection().getHiddenColumns()) { - int[] region = (int[]) av.getColumnSelection().getHiddenColumns() - .elementAt(i); - - hiddenColumns.addElement(new int[] + hiddenColumns.add(new int[] { region[0], region[1] }); } } @@ -954,7 +959,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); - g.translate(0, scrollOffset); + g.translate(0, getScrollOffset()); g.setColor(Color.black); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); @@ -968,7 +973,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, int ofontH = fontHeight; int sOffset = 0; int visHeight = 0; - int[] visr = (ap != null && ap.annotationPanel != null) ? ap.annotationPanel + int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel() .getVisibleVRange() : null; if (clip && visr != null) { @@ -1108,13 +1113,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (resizePanel) { - g.drawImage(image, 2, 0 - scrollOffset, this); + g.drawImage(image, 2, 0 - getScrollOffset(), this); } else if (dragEvent != null && aa != null) { g.setColor(Color.lightGray); g.drawString(aa[selectedRow].label, dragEvent.getX(), - dragEvent.getY() - scrollOffset); + dragEvent.getY() - getScrollOffset()); } if (!av.wrapAlignment && ((aa == null) || (aa.length < 1))) @@ -1124,4 +1129,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, 18); } } + + public int getScrollOffset() + { + return scrollOffset; + } }