X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=bb311efea67a97c6482d3db8df2e6eb17b95dffa;hb=af2dbf10bbcc54d9b9e4d398e9283b3c4a758e06;hp=e020701f5d281e36086babc1770120b7231143c4;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index e020701..bb311ef 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -54,7 +54,6 @@ import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.Scrollable; -import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; /** @@ -139,7 +138,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public AnnotationPanel(AlignmentPanel ap) { - MAC = new jalview.util.Platform().isAMac(); + MAC = jalview.util.Platform.isAMac(); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); @@ -241,7 +240,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public void adjustmentValueChanged(AdjustmentEvent evt) { // update annotation label display - ap.alabels.setScrollOffset(-evt.getValue()); + ap.getAlabels().setScrollOffset(-evt.getValue()); } /** @@ -289,14 +288,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (evt.getActionCommand().equals(REMOVE)) { - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int sel : av.getColumnSelection().getSelected()) { - anot[av.getColumnSelection().columnAt(i)] = null; + anot[sel] = null; } } else if (evt.getActionCommand().equals(LABEL)) { - String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL); + String exMesg = collectAnnotVals(anot, LABEL); String label = JOptionPane.showInputDialog(this, MessageManager.getString("label.enter_label"), exMesg); @@ -310,10 +309,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, aa[activeRow].hasText = true; } - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - int index = av.getColumnSelection().columnAt(i); - if (!av.getColumnSelection().isVisible(index)) { continue; @@ -335,12 +332,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, else if (evt.getActionCommand().equals(COLOUR)) { Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_foreground_colour"), Color.black); + MessageManager.getString("label.select_foreground_colour"), + Color.black); - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - int index = av.getColumnSelection().columnAt(i); - if (!av.getColumnSelection().isVisible(index)) { continue; @@ -398,10 +394,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, aa[activeRow].showAllColLabels = true; } } - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - int index = av.getColumnSelection().columnAt(i); - if (!av.getColumnSelection().isVisible(index)) { continue; @@ -412,7 +406,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, anot[index] = new Annotation(label, "", type, 0); } - anot[index].secondaryStructure = type != 'S' ? type : label .length() == 0 ? ' ' : label.charAt(0); anot[index].displayCharacter = label; @@ -428,16 +421,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } - private String collectAnnotVals(Annotation[] anot, - ColumnSelection columnSelection, String label2) + private String collectAnnotVals(Annotation[] anot, String label2) { String collatedInput = ""; String last = ""; ColumnSelection viscols = av.getColumnSelection(); // TODO: refactor and save av.getColumnSelection for efficiency - for (int i = 0; i < columnSelection.size(); i++) + for (int index : viscols.getSelected()) { - int index = columnSelection.columnAt(i); // always check for current display state - just in case if (!viscols.isVisible(index)) { @@ -519,7 +510,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } - if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1) + if (evt.isPopupTrigger() && activeRow != -1) { if (av.getColumnSelection() == null) { @@ -566,7 +557,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } - ap.scalePanel.mousePressed(evt); + ap.getScalePanel().mousePressed(evt); } @@ -582,7 +573,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, graphStretch = -1; graphStretchY = -1; mouseDragging = false; - ap.scalePanel.mouseReleased(evt); + ap.getScalePanel().mouseReleased(evt); } /** @@ -594,7 +585,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void mouseEntered(MouseEvent evt) { - ap.scalePanel.mouseEntered(evt); + ap.getScalePanel().mouseEntered(evt); } /** @@ -606,7 +597,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public void mouseExited(MouseEvent evt) { - ap.scalePanel.mouseExited(evt); + ap.getScalePanel().mouseExited(evt); } /** @@ -632,7 +623,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } else { - ap.scalePanel.mouseDragged(evt); + ap.getScalePanel().mouseDragged(evt); } } @@ -709,8 +700,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, && aa[row].annotations[res].description != null && aa[row].annotations[res].description.length() > 0) { - this.setToolTipText(JvSwingUtils - .wrapTooltip(true, aa[row].annotations[res].description)); + this.setToolTipText(JvSwingUtils.wrapTooltip(true, + aa[row].annotations[res].description)); } else { @@ -757,10 +748,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1, int y1) { - int pady = av.charHeight / 5; + int pady = av.getCharHeight() / 5; int charOffset = 0; graphics.setColor(Color.black); - graphics.fillRect(x1, y1, av.charWidth, av.charHeight); + graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight()); if (av.validCharWidth) { @@ -768,9 +759,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, char s = seq.getCharAt(res); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; + charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; graphics.drawString(String.valueOf(s), charOffset + x1, - (y1 + av.charHeight) - pady); + (y1 + av.getCharHeight()) - pady); } } @@ -799,7 +790,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } } - imgWidth = (av.endRes - av.startRes + 1) * av.charWidth; + imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth(); if (imgWidth < 1) { return; @@ -809,8 +800,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { try { - image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(), - BufferedImage.TYPE_INT_RGB); + image = new BufferedImage(imgWidth, ap.getAnnotationPanel() + .getHeight(), BufferedImage.TYPE_INT_RGB); } catch (OutOfMemoryError oom) { try @@ -867,7 +858,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } long stime = System.currentTimeMillis(); - gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0); + gg.copyArea(0, 0, imgWidth, getHeight(), + -horizontal * av.getCharWidth(), 0); long mtime = System.currentTimeMillis(); int sr = av.startRes; int er = av.endRes + 1; @@ -875,7 +867,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (horizontal > 0) // scrollbar pulled right, image to the left { - transX = (er - sr - horizontal) * av.charWidth; + transX = (er - sr - horizontal) * av.getCharWidth(); sr = er - horizontal; } else if (horizontal < 0) @@ -960,7 +952,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } g.setColor(Color.white); - g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight()); + g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight()); g.setFont(av.getFont()); if (fm == null) @@ -1013,9 +1005,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, @Override public int[] getVisibleVRange() { - if (ap != null && ap.alabels != null) + if (ap != null && ap.getAlabels() != null) { - int sOffset = -ap.alabels.scrollOffset; + int sOffset = -ap.getAlabels().getScrollOffset(); int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight(); bounds[0] = sOffset; bounds[1] = visHeight;