X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=af1ff7a4d87d4bb2bff91b5ef1f7b662263b4926;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=149f432f360dfb54b119ff3acd5505687e18178f;hpb=aa4c2cc89e5b9412f4b0211525b9aa76ea4a1920;p=jalview.git
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 149f432..af1ff7a 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,17 +1,17 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
* This program 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 2
* of the License, or (at your option) any later version.
- *
+ *
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -27,54 +27,69 @@ import jalview.datamodel.*;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class AnnotationPanel
- extends JPanel implements MouseListener,
- MouseMotionListener, ActionListener, AdjustmentListener
+public class AnnotationPanel extends JPanel implements MouseListener,
+ MouseMotionListener, ActionListener, AdjustmentListener
{
final String HELIX = "Helix";
+
final String SHEET = "Sheet";
+
final String LABEL = "Label";
+
final String REMOVE = "Remove Annotation";
+
final String COLOUR = "Colour";
+
final Color HELIX_COLOUR = Color.red.darker();
+
final Color SHEET_COLOUR = Color.green.darker().darker();
/** DOCUMENT ME!! */
AlignViewport av;
+
AlignmentPanel ap;
+
int activeRow = -1;
+
BufferedImage image;
+
BufferedImage fadedImage;
+
Graphics2D gg;
+
FontMetrics fm;
+
int imgWidth = 0;
+
boolean fastPaint = false;
- //Used For mouse Dragging and resizing graphs
+ // Used For mouse Dragging and resizing graphs
int graphStretch = -1;
+
int graphStretchY = -1;
- int min; //used by mouseDragged to see if user
- int max; //used by mouseDragged to see if user
+
+ int min; // used by mouseDragged to see if user
+
+ int max; // used by mouseDragged to see if user
+
boolean mouseDragging = false;
boolean MAC = false;
/**
* Creates a new AnnotationPanel object.
- *
- * @param ap DOCUMENT ME!
+ *
+ * @param ap
+ * DOCUMENT ME!
*/
public AnnotationPanel(AlignmentPanel ap)
{
- if (System.getProperty("os.name").startsWith("Mac"))
- {
- MAC = true;
- }
+ MAC = new jalview.util.Platform().isAMac();
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
@@ -84,7 +99,8 @@ public class AnnotationPanel
this.setLayout(null);
addMouseListener(this);
addMouseMotionListener(this);
- ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
+ ap.annotationScroller.getVerticalScrollBar()
+ .addAdjustmentListener(this);
}
public AnnotationPanel(AlignViewport av)
@@ -94,12 +110,13 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- ap.alabels.setScrollOffset( -evt.getValue());
+ ap.alabels.setScrollOffset(-evt.getValue());
}
/**
@@ -157,8 +174,9 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
@@ -183,14 +201,15 @@ public class AnnotationPanel
else if (evt.getActionCommand().equals(LABEL))
{
String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
- String label = JOptionPane.showInputDialog(this,"Enter label",exMesg);
-
+ String label = JOptionPane.showInputDialog(this, "Enter label",
+ exMesg);
+
if (label == null)
{
return;
}
- if ( (label.length() > 0) && !aa[activeRow].hasText)
+ if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
}
@@ -199,13 +218,18 @@ public class AnnotationPanel
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.colSel.isVisible(index))
continue;
if (anot[index] == null)
{
- anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that null exceptions aren't raised elsewhere.
- } else {
+ anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
+ // null exceptions
+ // aren't raised
+ // elsewhere.
+ }
+ else
+ {
anot[index].displayCharacter = label;
}
}
@@ -213,14 +237,13 @@ public class AnnotationPanel
else if (evt.getActionCommand().equals(COLOUR))
{
Color col = JColorChooser.showDialog(this,
- "Choose foreground colour",
- Color.black);
+ "Choose foreground colour", Color.black);
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.colSel.isVisible(index))
continue;
if (anot[index] == null)
@@ -231,7 +254,8 @@ public class AnnotationPanel
anot[index].colour = col;
}
}
- else // HELIX OR SHEET
+ else
+ // HELIX OR SHEET
{
char type = 0;
String symbol = "\u03B1";
@@ -252,15 +276,14 @@ public class AnnotationPanel
}
String label = JOptionPane.showInputDialog(
- "Enter a label for the structure?",
- symbol);
+ "Enter a label for the structure?", symbol);
if (label == null)
{
return;
}
- if ( (label.length() > 0) && !aa[activeRow].hasText)
+ if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
}
@@ -269,7 +292,7 @@ public class AnnotationPanel
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.colSel.isVisible(index))
continue;
if (anot[index] == null)
@@ -288,40 +311,43 @@ public class AnnotationPanel
return;
}
- private String collectAnnotVals(Annotation[] anot, ColumnSelection columnSelection,
- String label2)
+ private String collectAnnotVals(Annotation[] anot,
+ ColumnSelection columnSelection, String label2)
{
- String collatedInput="";
- String last="";
+ String collatedInput = "";
+ String last = "";
for (int i = 0; i < columnSelection.size(); i++)
{
int index = columnSelection.columnAt(i);
// always check for current display state - just in case
- if(!av.colSel.isVisible(index))
+ if (!av.colSel.isVisible(index))
continue;
- String tlabel=null;
+ String tlabel = null;
if (anot[index] != null)
{
- if (label2.equals(HELIX) || label2.equals(SHEET) || label2.equals(LABEL))
+ if (label2.equals(HELIX) || label2.equals(SHEET)
+ || label2.equals(LABEL))
{
tlabel = anot[index].description;
if (tlabel == null)
{
if (label2.equals(HELIX) || label2.equals(SHEET))
{
- tlabel = ""+anot[index].secondaryStructure;
- } else {
- tlabel = ""+anot[index].displayCharacter;
- }
+ tlabel = "" + anot[index].secondaryStructure;
+ }
+ else
+ {
+ tlabel = "" + anot[index].displayCharacter;
+ }
}
}
- if (tlabel!=null && !tlabel.equals(last))
+ if (tlabel != null && !tlabel.equals(last))
{
- if (last.length()>0)
+ if (last.length() > 0)
{
- collatedInput+=" ";
+ collatedInput += " ";
}
- collatedInput+=tlabel;
+ collatedInput += tlabel;
}
}
}
@@ -330,8 +356,9 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
@@ -360,7 +387,7 @@ public class AnnotationPanel
}
else if (aa[i].graph > 0)
{
- //Stretch Graph
+ // Stretch Graph
graphStretch = i;
graphStretchY = evt.getY();
}
@@ -408,8 +435,9 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
@@ -421,18 +449,20 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent evt)
{
- ap.scalePanel.mouseEntered(evt);
+ ap.scalePanel.mouseEntered(evt);
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent evt)
{
@@ -441,15 +471,16 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseDragged(MouseEvent evt)
{
if (graphStretch > -1)
{
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight +=
- graphStretchY - evt.getY();
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ - evt.getY();
if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)
{
av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
@@ -466,8 +497,9 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
@@ -510,19 +542,19 @@ public class AnnotationPanel
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
- if (aa[row].annotations != null
- && row > -1
- && res < (int) aa[row].annotations.length)
+ if (aa[row].annotations != null && row > -1
+ && res < (int) aa[row].annotations.length)
{
if (aa[row].graphGroup > -1)
{
StringBuffer tip = new StringBuffer("");
for (int gg = 0; gg < aa.length; gg++)
{
- if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res] != null)
+ if (aa[gg].graphGroup == aa[row].graphGroup
+ && aa[gg].annotations[res] != null)
{
- tip.append(aa[gg].label + " " + aa[gg].annotations[res].description +
- "
");
+ tip.append(aa[gg].label + " "
+ + aa[gg].annotations[res].description + "
");
}
}
if (tip.length() != 6)
@@ -532,15 +564,15 @@ public class AnnotationPanel
}
}
else if (aa[row].annotations[res] != null
- && aa[row].annotations[res].description != null)
+ && aa[row].annotations[res].description != null)
{
this.setToolTipText(aa[row].annotations[res].description);
}
if (aa[row].annotations[res] != null)
{
- StringBuffer text = new StringBuffer("Sequence position " +
- (res + 1));
+ StringBuffer text = new StringBuffer("Sequence position "
+ + (res + 1));
if (aa[row].annotations[res].description != null)
{
@@ -558,8 +590,9 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseClicked(MouseEvent evt)
{
@@ -567,8 +600,9 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
@@ -577,9 +611,8 @@ public class AnnotationPanel
if (image != null)
{
- if (fastPaint
- || (getVisibleRect().width != g.getClipBounds().width)
- || (getVisibleRect().height != g.getClipBounds().height))
+ if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
+ || (getVisibleRect().height != g.getClipBounds().height))
{
g.drawImage(image, 0, 0, this);
fastPaint = false;
@@ -587,19 +620,19 @@ public class AnnotationPanel
}
}
imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
- if (imgWidth<1)
+ if (imgWidth < 1)
return;
if (image == null || imgWidth != image.getWidth()
- || image.getHeight(this) != getHeight())
+ || image.getHeight(this) != getHeight())
{
image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
- BufferedImage.TYPE_INT_RGB);
+ BufferedImage.TYPE_INT_RGB);
gg = (Graphics2D) image.getGraphics();
if (av.antiAlias)
{
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ RenderingHints.VALUE_ANTIALIAS_ON);
}
gg.setFont(av.getFont());
@@ -613,23 +646,22 @@ public class AnnotationPanel
}
/**
- * DOCUMENT ME!
- *
- * @param horizontal DOCUMENT ME!
+ * non-Thread safe repaint
+ *
+ * @param horizontal
+ * repaint with horizontal shift in alignment
*/
public void fastPaint(int horizontal)
{
- if ( (horizontal == 0)
- || gg == null
- || av.alignment.getAlignmentAnnotation() == null
- || av.alignment.getAlignmentAnnotation().length < 1
- || av.updatingConsensus
- || av.updatingConservation)
+
+ if ((horizontal == 0) || gg == null
+ || av.alignment.getAlignmentAnnotation() == null
+ || av.alignment.getAlignmentAnnotation().length < 1
+ || av.updatingConsensus || av.updatingConservation)
{
repaint();
return;
}
-
gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
int sr = av.startRes;
@@ -650,20 +682,22 @@ public class AnnotationPanel
drawComponent(gg, sr, er);
- gg.translate( -transX, 0);
+ gg.translate(-transX, 0);
fastPaint = true;
-
repaint();
}
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startRes DOCUMENT ME!
- * @param endRes DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ * @param endRes
+ * DOCUMENT ME!
*/
public void drawComponent(Graphics g, int startRes, int endRes)
{
@@ -673,24 +707,21 @@ public class AnnotationPanel
{
return;
}
- //We'll keep a record of the old image,
- //and draw a faded image until the calculation
- //has completed
- if (fadedImage == null
- || fadedImage.getWidth() != imgWidth
- || fadedImage.getHeight() != image.getHeight())
+ // We'll keep a record of the old image,
+ // and draw a faded image until the calculation
+ // has completed
+ if (fadedImage == null || fadedImage.getWidth() != imgWidth
+ || fadedImage.getHeight() != image.getHeight())
{
- fadedImage = new BufferedImage(
- imgWidth, image.getHeight(),
- BufferedImage.TYPE_INT_RGB);
+ fadedImage = new BufferedImage(imgWidth, image.getHeight(),
+ BufferedImage.TYPE_INT_RGB);
Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
fadedG.setColor(Color.white);
fadedG.fillRect(0, 0, imgWidth, image.getHeight());
- fadedG.setComposite(
- AlphaComposite.getInstance(
+ fadedG.setComposite(AlphaComposite.getInstance(
AlphaComposite.SRC_OVER, .3f));
fadedG.drawImage(image, 0, 0, this);
@@ -711,8 +742,8 @@ public class AnnotationPanel
fm = g.getFontMetrics();
}
- if ( (av.alignment.getAlignmentAnnotation() == null) ||
- (av.alignment.getAlignmentAnnotation().length < 1))
+ if ((av.alignment.getAlignmentAnnotation() == null)
+ || (av.alignment.getAlignmentAnnotation().length < 1))
{
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
@@ -727,16 +758,16 @@ public class AnnotationPanel
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- int x = 0, y=0;
+ int x = 0, y = 0;
int column = 0;
char lastSS;
int lastSSX;
int iconOffset = 0;
boolean validRes = false;
-
+ boolean validEnd = false;
boolean[] graphGroupDrawn = new boolean[aa.length];
- //\u03B2 \u03B1
+ // \u03B2 \u03B1
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
@@ -761,13 +792,13 @@ public class AnnotationPanel
if (row.hasText)
{
- iconOffset =av.charHeight -fm.getDescent();
+ iconOffset = av.charHeight - fm.getDescent();
y -= av.charHeight;
}
}
else if (row.hasText)
{
- iconOffset = av.charHeight -fm.getDescent();
+ iconOffset = av.charHeight - fm.getDescent();
}
else
@@ -775,29 +806,27 @@ public class AnnotationPanel
iconOffset = 0;
}
-
if (av.updatingConsensus && aa[i] == av.consensus)
{
y += av.charHeight;
- g.drawImage(fadedImage,
- 0, y - row.height, imgWidth, y,
- 0, y - row.height, imgWidth, y, this);
+ g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
+ - row.height, imgWidth, y, this);
g.setColor(Color.black);
// g.drawString("Calculating Consensus....",20, y-row.height/2);
continue;
}
- else if (av.updatingConservation && aa[i].label.equals("Conservation"))
+ else if (av.updatingConservation
+ && aa[i].label.equals("Conservation"))
{
y += av.charHeight;
- g.drawImage(fadedImage,
- 0, y - row.height, imgWidth, y,
- 0, y - row.height, imgWidth, y, this);
+ g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
+ - row.height, imgWidth, y, this);
g.setColor(Color.black);
- // g.drawString("Calculating Conservation.....",20, y-row.height/2);
+ // g.drawString("Calculating Conservation.....",20, y-row.height/2);
continue;
}
@@ -805,23 +834,21 @@ public class AnnotationPanel
{
y += av.charHeight;
- g.drawImage(fadedImage,
- 0, y - row.height, imgWidth, y,
- 0, y - row.height, imgWidth, y, this);
+ g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
+ - row.height, imgWidth, y, this);
g.setColor(Color.black);
- /// g.drawString("Calculating Quality....",20, y-row.height/2);
+ // / g.drawString("Calculating Quality....",20, y-row.height/2);
continue;
}
-
-
x = 0;
while (x < endRes - startRes)
{
if (av.hasHiddenColumns)
{
- column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
+ column = av.getColumnSelection().adjustForHiddenColumns(
+ startRes + x);
if (column > row.annotations.length - 1)
{
break;
@@ -832,8 +859,7 @@ public class AnnotationPanel
column = startRes + x;
}
- if ( (row.annotations==null)
- || (row.annotations.length <= column)
+ if ((row.annotations == null) || (row.annotations.length <= column)
|| (row.annotations[column] == null))
{
validRes = false;
@@ -855,22 +881,26 @@ public class AnnotationPanel
if (v == column)
{
- g.fillRect(x * av.charWidth, y,
- av.charWidth, av.charHeight);
+ g
+ .fillRect(x * av.charWidth, y, av.charWidth,
+ av.charHeight);
}
}
}
}
if (av.validCharWidth && validRes
- && row.annotations[column].displayCharacter != null
- && (row.annotations[column].displayCharacter.length() > 0))
+ && row.annotations[column].displayCharacter != null
+ && (row.annotations[column].displayCharacter.length() > 0))
{
- int charOffset = (av.charWidth -
- fm.charWidth(row.annotations[column].
- displayCharacter.charAt(
- 0))) / 2;
+ int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth - fm
+ .charsWidth(row.annotations[column].displayCharacter
+ .toCharArray(), 0,
+ row.annotations[column].displayCharacter.length())) / 2)
+ : (av.charWidth - fm
+ .charWidth(row.annotations[column].displayCharacter
+ .charAt(0))) / 2;
if (row.annotations[column].colour == null)
g.setColor(Color.black);
@@ -880,87 +910,78 @@ public class AnnotationPanel
if (column == 0 || row.graph > 0)
{
g.drawString(row.annotations[column].displayCharacter,
- (x * av.charWidth) + charOffset,
- y + iconOffset);
+ (x * av.charWidth) + charOffset, y + iconOffset);
}
- else if (
- row.annotations[column - 1] == null
- || (!row.annotations[column].displayCharacter.equals(
- row.annotations[column - 1].displayCharacter)
- ||
- (row.annotations[column].displayCharacter.length() < 2 &&
- row.annotations[column].secondaryStructure == ' ')))
+ else if (row.annotations[column - 1] == null
+ || (!row.annotations[column].displayCharacter
+ .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
+ .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
{
- g.drawString(row.annotations[column].displayCharacter,
- x * av.charWidth + charOffset,
- y + iconOffset);
+ g.drawString(row.annotations[column].displayCharacter, x
+ * av.charWidth + charOffset, y + iconOffset);
}
}
if (row.hasIcons)
{
- if (!validRes ||
- (row.annotations[column].secondaryStructure != lastSS))
+ if (!validRes
+ || (row.annotations[column].secondaryStructure != lastSS))
{
switch (lastSS)
{
- case 'H':
- g.setColor(HELIX_COLOUR);
- if (MAC)
- {
- //Off by 1 offset when drawing rects and ovals
- //to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX, 7, 8, 8);
- break;
- }
-
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
-
- if (sCol == 0 ||
- row.annotations[sCol - 1] == null ||
- row.annotations[sCol - 1].secondaryStructure != 'H')
- {
- g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
- 180);
- x1 += av.charWidth / 2;
- }
-
- if (row.annotations[column] == null ||
- row.annotations[column].secondaryStructure != 'H')
- {
- g.fillArc( (x * av.charWidth) - av.charWidth,
- y + 4 + iconOffset, av.charWidth, 8, 270, 180);
- x2 -= av.charWidth / 2;
- }
-
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+ case 'H':
+ g.setColor(HELIX_COLOUR);
+ if (MAC)
+ {
+ // Off by 1 offset when drawing rects and ovals
+ // to offscreen image on the MAC
+ g.fillRoundRect(lastSSX, y + 4 + iconOffset,
+ (x * av.charWidth) - lastSSX, 7, 8, 8);
break;
+ }
- case 'E':
- g.setColor(SHEET_COLOUR);
- g.fillRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX - 4, 7);
- g.fillPolygon(new int[]
- { (x * av.charWidth) - 4,
- (x * av.charWidth) - 4,
- (x * av.charWidth)},
- new int[]
- {
- y + iconOffset, y + 14 + iconOffset,
- y + 8 + iconOffset
- }, 3);
+ int sCol = (lastSSX / av.charWidth) + startRes;
+ int x1 = lastSSX;
+ int x2 = (x * av.charWidth);
- break;
+ if (sCol == 0
+ || row.annotations[sCol - 1] == null
+ || row.annotations[sCol - 1].secondaryStructure != 'H')
+ {
+ g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
+ 180);
+ x1 += av.charWidth / 2;
+ }
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset,
- (x * av.charWidth) - lastSSX, 2);
+ if (row.annotations[column] == null
+ || row.annotations[column].secondaryStructure != 'H')
+ {
+ g.fillArc((x * av.charWidth) - av.charWidth, y + 4
+ + iconOffset, av.charWidth, 8, 270, 180);
+ x2 -= av.charWidth / 2;
+ }
- break;
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+ break;
+
+ case 'E':
+ g.setColor(SHEET_COLOUR);
+ g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
+ - lastSSX - 4, 7);
+ g.fillPolygon(new int[]
+ { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
+ (x * av.charWidth) }, new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+ 3);
+
+ break;
+
+ default:
+ g.setColor(Color.gray);
+ g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+ - lastSSX, 2);
+
+ break;
}
if (validRes)
@@ -983,81 +1004,81 @@ public class AnnotationPanel
if (column >= row.annotations.length)
{
column = row.annotations.length - 1;
+ validEnd = false;
+ }
+ else
+ {
+ validEnd = true;
}
- // x ++;
+ // x ++;
if (row.hasIcons)
{
switch (lastSS)
{
- case 'H':
- g.setColor(HELIX_COLOUR);
- if (MAC)
- {
- //Off by 1 offset when drawing rects and ovals
- //to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX, 7, 8, 8);
- break;
- }
+ case 'H':
+ g.setColor(HELIX_COLOUR);
+ if (MAC)
+ {
+ // Off by 1 offset when drawing rects and ovals
+ // to offscreen image on the MAC
+ g.fillRoundRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
+ - lastSSX, 7, 8, 8);
+ break;
+ }
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
+ int sCol = (lastSSX / av.charWidth) + startRes;
+ int x1 = lastSSX;
+ int x2 = (x * av.charWidth);
- if (sCol == 0 ||
- row.annotations[sCol - 1] == null ||
- row.annotations[sCol - 1].secondaryStructure != 'H')
- {
- g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
- x1 += av.charWidth / 2;
- }
+ if (sCol == 0 || row.annotations[sCol - 1] == null
+ || row.annotations[sCol - 1].secondaryStructure != 'H')
+ {
+ g
+ .fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8,
+ 90, 180);
+ x1 += av.charWidth / 2;
+ }
- if (row.annotations[column] == null ||
- row.annotations[column].secondaryStructure != 'H')
- {
- g.fillArc( (x * av.charWidth) - av.charWidth,
- y + 4 + iconOffset, av.charWidth, 8, 270,
- 180);
- x2 -= av.charWidth / 2;
- }
+ if (row.annotations[column] == null
+ || row.annotations[column].secondaryStructure != 'H')
+ {
+ g.fillArc((x * av.charWidth) - av.charWidth,
+ y + 4 + iconOffset, av.charWidth, 8, 270, 180);
+ x2 -= av.charWidth / 2;
+ }
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
- break;
+ break;
- case 'E':
- g.setColor(SHEET_COLOUR);
+ case 'E':
+ g.setColor(SHEET_COLOUR);
- if (row.annotations[endRes] == null
- || row.annotations[endRes].secondaryStructure != 'E')
- {
- g.fillRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX - 4, 7);
- g.fillPolygon(new int[]
- { (x * av.charWidth) - 4,
- (x * av.charWidth) - 4,
- (x * av.charWidth)},
- new int[]
- {
- y + iconOffset, y + 14 + iconOffset,
- y + 7 + iconOffset
- }, 3);
- }
- else
- {
- g.fillRect(lastSSX, y + 4 + iconOffset,
- (x + 1) * av.charWidth - lastSSX, 7);
- }
- break;
+ if (!validEnd || row.annotations[endRes] == null
+ || row.annotations[endRes].secondaryStructure != 'E')
+ {
+ g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
+ - lastSSX - 4, 7);
+ g.fillPolygon(new int[]
+ { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
+ (x * av.charWidth) }, new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3);
+ }
+ else
+ {
+ g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * av.charWidth
+ - lastSSX, 7);
+ }
+ break;
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset,
- (x * av.charWidth) - lastSSX, 2);
+ default:
+ g.setColor(Color.gray);
+ g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+ - lastSSX, 2);
- break;
+ break;
}
}
@@ -1094,9 +1115,8 @@ public class AnnotationPanel
{
if (aa[gg].graphGroup == row.graphGroup)
{
- drawLineGraph(g, aa[gg], startRes, endRes, y,
- groupmin, groupmax,
- row.graphHeight);
+ drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
+ groupmax, row.graphHeight);
}
}
@@ -1104,14 +1124,14 @@ public class AnnotationPanel
}
else
{
- drawLineGraph(g, row, startRes, endRes,
- y, row.graphMin, row.graphMax, row.graphHeight);
+ drawLineGraph(g, row, startRes, endRes, y, row.graphMin,
+ row.graphMax, row.graphHeight);
}
}
else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
- drawBarGraph(g, row, startRes, endRes,
- row.graphMin, row.graphMax, y);
+ drawBarGraph(g, row, startRes, endRes, row.graphMin,
+ row.graphMax, y);
}
}
@@ -1127,11 +1147,8 @@ public class AnnotationPanel
}
}
- public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
- int sRes, int eRes,
- int y,
- float min, float max,
- int graphHeight)
+ public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+ int eRes, int y, float min, float max, int graphHeight)
{
if (sRes > aa.annotations.length)
{
@@ -1140,7 +1157,7 @@ public class AnnotationPanel
int x = 0;
- //Adjustment for fastpaint to left
+ // Adjustment for fastpaint to left
if (eRes < av.endRes)
{
eRes++;
@@ -1156,10 +1173,10 @@ public class AnnotationPanel
int y1 = y, y2 = y;
float range = max - min;
- ////Draw origin
+ // //Draw origin
if (min < 0)
{
- y2 = y - (int) ( (0 - min / range) * graphHeight);
+ y2 = y - (int) ((0 - min / range) * graphHeight);
}
g.setColor(Color.gray);
@@ -1183,7 +1200,8 @@ public class AnnotationPanel
break;
}
- if (aa.annotations[column] == null || aa.annotations[column - 1] == null)
+ if (aa.annotations[column] == null
+ || aa.annotations[column - 1] == null)
{
x++;
continue;
@@ -1194,13 +1212,13 @@ public class AnnotationPanel
else
g.setColor(aa.annotations[column].colour);
- y1 = y -
- (int) ( ( (aa.annotations[column - 1].value - min) / range) * graphHeight);
- y2 = y -
- (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight);
+ y1 = y
+ - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
+ y2 = y
+ - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
- g.drawLine(x * av.charWidth - av.charWidth / 2, y1,
- x * av.charWidth + av.charWidth / 2, y2);
+ g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth
+ + av.charWidth / 2, y2);
x++;
}
@@ -1208,22 +1226,18 @@ public class AnnotationPanel
{
g.setColor(aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
- g2.setStroke(new BasicStroke(1,
- BasicStroke.CAP_SQUARE,
- BasicStroke.JOIN_ROUND, 3f,
- new float[]
- {5f, 3f}, 0f));
+ g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
- y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight);
+ y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight);
g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
- int sRes, int eRes,
- float min, float max,
- int y)
+ public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+ int eRes, float min, float max, int y)
{
if (sRes > aa.annotations.length)
{
@@ -1238,7 +1252,7 @@ public class AnnotationPanel
if (min < 0)
{
- y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);
+ y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
}
g.setColor(Color.gray);
@@ -1272,8 +1286,8 @@ public class AnnotationPanel
else
g.setColor(aa.annotations[column].colour);
- y1 = y -
- (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
+ y1 = y
+ - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
if (y1 - y2 > 0)
{
@@ -1291,21 +1305,19 @@ public class AnnotationPanel
{
g.setColor(aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
- g2.setStroke(new BasicStroke(1,
- BasicStroke.CAP_SQUARE,
- BasicStroke.JOIN_ROUND, 3f,
- new float[]
- {5f, 3f}, 0f));
+ g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
- y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight);
+ y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
// used by overview window
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y,
- int sRes, int eRes)
+ public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
+ int y, int sRes, int eRes)
{
eRes = Math.min(eRes, aa.annotations.length);
g.setColor(Color.white);
@@ -1323,7 +1335,7 @@ public class AnnotationPanel
else
g.setColor(aa.annotations[j].colour);
- height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);
+ height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
if (height > y)
{
height = y;