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JAL-967, JAL-1114, JAL-1115 - modified render and calculation api to work on bare...
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Thu, 7 Jun 2012 09:44:43 +0000
(10:44 +0100)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Thu, 7 Jun 2012 09:56:34 +0000
(10:56 +0100)
src/jalview/analysis/AAFrequency.java
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src/jalview/appletgui/OverviewPanel.java
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src/jalview/gui/OverviewPanel.java
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src/jalview/renderer/AnnotationRenderer.java
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diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
375504d
..
7e77b0f
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-219,33
+219,40
@@
public class AAFrequency
}
for (int i = iStart; i < width; i++)
{
}
for (int i = iStart; i < width; i++)
{
- if (i >= hconsensus.length)
+ Hashtable hci;
+ if (i >= hconsensus.length || ((hci=hconsensus[i])==null))
{
// happens if sequences calculated over were shorter than alignment
// width
consensus.annotations[i] = null;
continue;
}
{
// happens if sequences calculated over were shorter than alignment
// width
consensus.annotations[i] = null;
continue;
}
+
value = 0;
value = 0;
+ Float fv;
if (ignoreGapsInConsensusCalculation)
{
if (ignoreGapsInConsensusCalculation)
{
- value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS))
- .floatValue();
+ fv = (Float) hci.get(AAFrequency.PID_NOGAPS);
}
else
{
}
else
{
- value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS))
- .floatValue();
+ fv = (Float) hci.get(AAFrequency.PID_GAPS);
}
}
-
- String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
- String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
+ if (fv==null)
+ {
+ consensus.annotations[i] = null;
+ // data has changed below us .. give up and
+ continue;
+ }
+ value = fv.floatValue();
+ String maxRes = hci.get(AAFrequency.MAXRESIDUE).toString();
+ String mouseOver = hci.get(AAFrequency.MAXRESIDUE) + " ";
if (maxRes.length() > 1)
{
mouseOver = "[" + maxRes + "] ";
maxRes = "+";
}
if (maxRes.length() > 1)
{
mouseOver = "[" + maxRes + "] ";
maxRes = "+";
}
- int[][] profile = (int[][]) hconsensus[i].get(AAFrequency.PROFILE);
+ int[][] profile = (int[][]) hci.get(AAFrequency.PROFILE);
if (profile != null && includeAllConsSymbols)
{
mouseOver = "";
if (profile != null && includeAllConsSymbols)
{
mouseOver = "";
diff --git
a/src/jalview/appletgui/OverviewPanel.java
b/src/jalview/appletgui/OverviewPanel.java
index
4b646c3
..
ba066a1
100755
(executable)
--- a/
src/jalview/appletgui/OverviewPanel.java
+++ b/
src/jalview/appletgui/OverviewPanel.java
@@
-367,7
+367,7
@@
public class OverviewPanel extends Panel implements Runnable,
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);
- ap.annotationPanel.renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+ ap.annotationPanel.renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations,
(int) (sampleCol) + 1, graphHeight,
(int) (col * sampleCol), (int) (col * sampleCol) + 1);
mg.translate(-col, -sequencesHeight);
(int) (sampleCol) + 1, graphHeight,
(int) (col * sampleCol), (int) (col * sampleCol) + 1);
mg.translate(-col, -sequencesHeight);
diff --git
a/src/jalview/gui/OverviewPanel.java
b/src/jalview/gui/OverviewPanel.java
index
c844315
..
475f0c7
100755
(executable)
--- a/
src/jalview/gui/OverviewPanel.java
+++ b/
src/jalview/gui/OverviewPanel.java
@@
-1,18
+1,18
@@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ *
* This file is part of Jalview.
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview 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
+ *
+ * Jalview 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.
* PURPOSE. See the GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
@@
-26,7
+26,7
@@
import javax.swing.*;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
* @author $author$
* @version $Revision$
*/
@@
-67,7
+67,7
@@
public class OverviewPanel extends JPanel implements Runnable
/**
* Creates a new OverviewPanel object.
/**
* Creates a new OverviewPanel object.
- *
+ *
* @param ap
* DOCUMENT ME!
*/
* @param ap
* DOCUMENT ME!
*/
@@
-115,6
+115,7
@@
public class OverviewPanel extends JPanel implements Runnable
addComponentListener(new ComponentAdapter()
{
addComponentListener(new ComponentAdapter()
{
+ @Override
public void componentResized(ComponentEvent evt)
{
if ((getWidth() != width)
public void componentResized(ComponentEvent evt)
{
if ((getWidth() != width)
@@
-127,6
+128,7
@@
public class OverviewPanel extends JPanel implements Runnable
addMouseMotionListener(new MouseMotionAdapter()
{
addMouseMotionListener(new MouseMotionAdapter()
{
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (!av.wrapAlignment)
public void mouseDragged(MouseEvent evt)
{
if (!av.wrapAlignment)
@@
-142,6
+144,7
@@
public class OverviewPanel extends JPanel implements Runnable
addMouseListener(new MouseAdapter()
{
addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
if (!av.wrapAlignment)
public void mousePressed(MouseEvent evt)
{
if (!av.wrapAlignment)
@@
-242,6
+245,7
@@
public class OverviewPanel extends JPanel implements Runnable
/**
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
*/
+ @Override
public void run()
{
miniMe = null;
public void run()
{
miniMe = null;
@@
-359,13
+363,13
@@
public class OverviewPanel extends JPanel implements Runnable
if (av.getAlignmentConservationAnnotation()!= null)
{
if (av.getAlignmentConservationAnnotation()!= null)
{
- renderer.updateFromAlignViewport(av);
+ renderer.updateFromAlignViewport(av);
for (col = 0; col < width; col++)
{
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);
for (col = 0; col < width; col++)
{
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);
- renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+ renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations,
(int) (sampleCol) + 1, graphHeight,
(int) (col * sampleCol), (int) (col * sampleCol) + 1);
mg.translate(-col, -sequencesHeight);
(int) (sampleCol) + 1, graphHeight,
(int) (col * sampleCol), (int) (col * sampleCol) + 1);
mg.translate(-col, -sequencesHeight);
@@
-438,10
+442,11
@@
public class OverviewPanel extends JPanel implements Runnable
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
- *
+ *
* @param g
* DOCUMENT ME!
*/
* @param g
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
if (resizing)
public void paintComponent(Graphics g)
{
if (resizing)
diff --git
a/src/jalview/renderer/AnnotationRenderer.java
b/src/jalview/renderer/AnnotationRenderer.java
index
ace94f4
..
cfdfdf6
100644
(file)
--- a/
src/jalview/renderer/AnnotationRenderer.java
+++ b/
src/jalview/renderer/AnnotationRenderer.java
@@
-4,6
+4,7
@@
import jalview.analysis.AAFrequency;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.schemes.ColourSchemeI;
import jalview.datamodel.ColumnSelection;
import jalview.schemes.ColourSchemeI;
@@
-29,7
+30,7
@@
public class AnnotationRenderer
// TODO Auto-generated constructor stub
}
// TODO Auto-generated constructor stub
}
- public void drawStemAnnot(Graphics g, AlignmentAnnotation row,
+ public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
@@
-39,21
+40,21
@@
public class AnnotationRenderer
int x2 = (x * charWidth);
Regex closeparen = new Regex("(\\))");
int x2 = (x * charWidth);
Regex closeparen = new Regex("(\\))");
- String dc = (column == 0 || row.annotations[column - 1] == null) ? ""
- : row.annotations[column - 1].displayCharacter;
+ String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
+ : row_annotations[column - 1].displayCharacter;
- boolean diffupstream = sCol == 0 || row.annotations[sCol - 1] == null
- || !dc.equals(row.annotations[sCol - 1].displayCharacter);
+ boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
+ || !dc.equals(row_annotations[sCol - 1].displayCharacter);
boolean diffdownstream = !validRes || !validEnd
boolean diffdownstream = !validRes || !validEnd
- || row.annotations[column] == null
- || !dc.equals(row.annotations[column].displayCharacter);
+ || row_annotations[column] == null
+ || !dc.equals(row_annotations[column].displayCharacter);
// System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
// If a closing base pair half of the stem, display a backward arrow
if (column > 0 && closeparen.search(dc))
{
if (diffupstream)
// System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
// If a closing base pair half of the stem, display a backward arrow
if (column > 0 && closeparen.search(dc))
{
if (diffupstream)
- // if (validRes && column>1 && row.annotations[column-2]!=null &&
- // dc.equals(row.annotations[column-2].displayCharacter))
+ // if (validRes && column>1 && row_annotations[column-2]!=null &&
+ // dc.equals(row_annotations[column-2].displayCharacter))
{
g.fillPolygon(new int[]
{ lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
{
g.fillPolygon(new int[]
{ lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
@@
-252,7
+253,7
@@
public class AnnotationRenderer
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
-
+ Annotation[] row_annotations=row.annotations;
if (!row.visible)
{
continue;
if (!row.visible)
{
continue;
@@
-329,7
+330,7
@@
public class AnnotationRenderer
if (hasHiddenColumns)
{
column = columnSelection.adjustForHiddenColumns(startRes + x);
if (hasHiddenColumns)
{
column = columnSelection.adjustForHiddenColumns(startRes + x);
- if (column > row.annotations.length - 1)
+ if (column > row_annotations.length - 1)
{
break;
}
{
break;
}
@@
-339,8
+340,8
@@
public class AnnotationRenderer
column = startRes + x;
}
column = startRes + x;
}
- if ((row.annotations == null) || (row.annotations.length <= column)
- || (row.annotations[column] == null))
+ if ((row_annotations == null) || (row_annotations.length <= column)
+ || (row_annotations[column] == null))
{
validRes = false;
}
{
validRes = false;
}
@@
-375,16
+376,16
@@
public class AnnotationRenderer
}
if (validCharWidth
&& validRes
}
if (validCharWidth
&& validRes
- && row.annotations[column].displayCharacter != null
- && (row.annotations[column].displayCharacter.length() > 0))
+ && row_annotations[column].displayCharacter != null
+ && (row_annotations[column].displayCharacter.length() > 0))
{
if (centreColLabels || scaleColLabel)
{
{
if (centreColLabels || scaleColLabel)
{
- fmWidth = (float) fm.charsWidth(
- row.annotations[column].displayCharacter
+ fmWidth = fm.charsWidth(
+ row_annotations[column].displayCharacter
.toCharArray(), 0,
.toCharArray(), 0,
- row.annotations[column].displayCharacter.length());
+ row_annotations[column].displayCharacter.length());
if (scaleColLabel)
{
if (scaleColLabel)
{
@@
-403,29
+404,29
@@
public class AnnotationRenderer
}
else
{
}
else
{
- fmWidth = (float) fm
- .charWidth(row.annotations[column].displayCharacter
+ fmWidth = fm
+ .charWidth(row_annotations[column].displayCharacter
.charAt(0));
}
charOffset = (int) ((charWidth - fmWidth) / 2f);
.charAt(0));
}
charOffset = (int) ((charWidth - fmWidth) / 2f);
- if (row.annotations[column].colour == null)
+ if (row_annotations[column].colour == null)
g.setColor(Color.black);
else
g.setColor(Color.black);
else
- g.setColor(row.annotations[column].colour);
+ g.setColor(row_annotations[column].colour);
if (column == 0 || row.graph > 0)
{
if (column == 0 || row.graph > 0)
{
- g.drawString(row.annotations[column].displayCharacter,
+ g.drawString(row_annotations[column].displayCharacter,
(x * charWidth) + charOffset, y + iconOffset);
}
(x * charWidth) + charOffset, y + iconOffset);
}
- else if (row.annotations[column - 1] == null
+ else if (row_annotations[column - 1] == null
|| (labelAllCols
|| (labelAllCols
- || !row.annotations[column].displayCharacter
- .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
- .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
+ || !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
+ g.drawString(row_annotations[column].displayCharacter, x
* charWidth + charOffset, y + iconOffset);
}
g.setFont(ofont);
* charWidth + charOffset, y + iconOffset);
}
g.setFont(ofont);
@@
-433,12
+434,12
@@
public class AnnotationRenderer
}
if (row.hasIcons)
{
}
if (row.hasIcons)
{
- char ss = validRes ? row.annotations[column].secondaryStructure
+ char ss = validRes ? row_annotations[column].secondaryStructure
: ' ';
if (ss == 'S')
{
// distinguish between forward/backward base-pairing
: ' ';
if (ss == 'S')
{
// distinguish between forward/backward base-pairing
- if (row.annotations[column].displayCharacter.indexOf(')') > -1)
+ if (row_annotations[column].displayCharacter.indexOf(')') > -1)
{
ss = 's';
}
{
ss = 's';
}
@@
-450,18
+451,18
@@
public class AnnotationRenderer
switch (lastSS)
{
case 'H':
switch (lastSS)
{
case 'H':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
case 'E':
column, validRes, validEnd);
break;
case 'E':
- drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
case 'S': // Stem case for RNA secondary structure
case 's': // and opposite direction
column, validRes, validEnd);
break;
case 'S': // Stem case for RNA secondary structure
case 's': // and opposite direction
- drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
column, validRes, validEnd);
break;
@@
-490,17
+491,17
@@
public class AnnotationRenderer
column++;
x++;
}
column++;
x++;
}
- if (column >= row.annotations.length)
+ if (column >= row_annotations.length)
{
{
- column = row.annotations.length - 1;
+ column = row_annotations.length - 1;
validEnd = false;
}
else
{
validEnd = true;
}
validEnd = false;
}
else
{
validEnd = true;
}
- if ((row.annotations == null) || (row.annotations.length <= column)
- || (row.annotations[column] == null))
+ if ((row_annotations == null) || (row_annotations.length <= column)
+ || (row_annotations[column] == null))
{
validRes = false;
}
{
validRes = false;
}
@@
-516,21
+517,21
@@
public class AnnotationRenderer
switch (lastSS)
{
case 'H':
switch (lastSS)
{
case 'H':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
case 'E':
column, validRes, validEnd);
break;
case 'E':
- drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
case 's':
case 'S': // Stem case for RNA secondary structure
column, validRes, validEnd);
break;
case 's':
case 'S': // Stem case for RNA secondary structure
- drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
default:
column, validRes, validEnd);
break;
default:
- drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
+ drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
}
column, validRes, validEnd);
break;
}
@@
-569,7
+570,7
@@
public class AnnotationRenderer
{
if (aa[gg].graphGroup == row.graphGroup)
{
{
if (aa[gg].graphGroup == row.graphGroup)
{
- drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
+ drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin,
groupmax, row.graphHeight);
}
}
groupmax, row.graphHeight);
}
}
@@
-578,13
+579,13
@@
public class AnnotationRenderer
}
else
{
}
else
{
- drawLineGraph(g, row, startRes, endRes, y, row.graphMin,
+ drawLineGraph(g, row, row_annotations, startRes, endRes, y, row.graphMin,
row.graphMax, row.graphHeight);
}
}
else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
row.graphMax, row.graphHeight);
}
}
else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
- drawBarGraph(g, row, startRes, endRes, row.graphMin,
+ drawBarGraph(g, row, row_annotations, startRes, endRes, row.graphMin,
row.graphMax, y);
}
}
row.graphMax, y);
}
}
@@
-609,7
+610,7
@@
public class AnnotationRenderer
private Color STEM_COLOUR = Color.blue;
private Color STEM_COLOUR = Color.blue;
- public void drawGlyphLine(Graphics g, AlignmentAnnotation row,
+ public void drawGlyphLine(Graphics g, Annotation[] row,
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
@@
-617,14
+618,14
@@
public class AnnotationRenderer
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
}
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
}
- public void drawSheetAnnot(Graphics g, AlignmentAnnotation row,
+ public void drawSheetAnnot(Graphics g, Annotation[] row,
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
g.setColor(SHEET_COLOUR);
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
g.setColor(SHEET_COLOUR);
- if (!validEnd || !validRes || row.annotations[column] == null
- || row.annotations[column].secondaryStructure != 'E')
+ if (!validEnd || !validRes || row==null || row[column] == null
+ || row[column].secondaryStructure != 'E')
{
g.fillRect(lastSSX, y + 4 + iconOffset,
(x * charWidth) - lastSSX - 4, 7);
{
g.fillRect(lastSSX, y + 4 + iconOffset,
(x * charWidth) - lastSSX - 4, 7);
@@
-642,7
+643,7
@@
public class AnnotationRenderer
}
}
- public void drawHelixAnnot(Graphics g, AlignmentAnnotation row,
+ public void drawHelixAnnot(Graphics g, Annotation[] row,
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
@@
-658,8
+659,8
@@
public class AnnotationRenderer
// Off by 1 offset when drawing rects and ovals
// to offscreen image on the MAC
g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
// Off by 1 offset when drawing rects and ovals
// to offscreen image on the MAC
g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
- if (sCol == 0 || row.annotations[sCol - 1] == null
- || row.annotations[sCol - 1].secondaryStructure != 'H')
+ if (sCol == 0 || row[sCol - 1] == null
+ || row[sCol - 1].secondaryStructure != 'H')
{
}
else
{
}
else
@@
-668,8
+669,8
@@
public class AnnotationRenderer
g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
0, 0);
}
g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
0, 0);
}
- if (!validRes || row.annotations[column] == null
- || row.annotations[column].secondaryStructure != 'H')
+ if (!validRes || row[column] == null
+ || row[column].secondaryStructure != 'H')
{
}
{
}
@@
-684,15
+685,15
@@
public class AnnotationRenderer
return;
}
return;
}
- if (sCol == 0 || row.annotations[sCol - 1] == null
- || row.annotations[sCol - 1].secondaryStructure != 'H')
+ if (sCol == 0 || row[sCol - 1] == null
+ || row[sCol - 1].secondaryStructure != 'H')
{
g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
x1 += charWidth / 2;
}
{
g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
x1 += charWidth / 2;
}
- if (!validRes || row.annotations[column] == null
- || row.annotations[column].secondaryStructure != 'H')
+ if (!validRes || row[column] == null
+ || row[column].secondaryStructure != 'H')
{
g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
8, 270, 180);
{
g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
8, 270, 180);
@@
-702,10
+703,10
@@
public class AnnotationRenderer
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
}
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
}
- public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+ public void drawLineGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
int eRes, int y, float min, float max, int graphHeight)
{
int eRes, int y, float min, float max, int graphHeight)
{
- if (sRes > aa.annotations.length)
+ if (sRes > aa_annotations.length)
{
return;
}
{
return;
}
@@
-718,7
+719,7
@@
public class AnnotationRenderer
eRes++;
}
eRes++;
}
- eRes = Math.min(eRes, aa.annotations.length);
+ eRes = Math.min(eRes, aa_annotations.length);
if (sRes == 0)
{
if (sRes == 0)
{
@@
-737,10
+738,10
@@
public class AnnotationRenderer
g.setColor(Color.gray);
g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
g.setColor(Color.gray);
g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
- eRes = Math.min(eRes, aa.annotations.length);
+ eRes = Math.min(eRes, aa_annotations.length);
int column;
int column;
- int aaMax = aa.annotations.length - 1;
+ int aaMax = aa_annotations.length - 1;
while (x < eRes - sRes)
{
while (x < eRes - sRes)
{
@@
-755,51
+756,51
@@
public class AnnotationRenderer
break;
}
break;
}
- if (aa.annotations[column] == null
- || aa.annotations[column - 1] == null)
+ if (aa_annotations[column] == null
+ || aa_annotations[column - 1] == null)
{
x++;
continue;
}
{
x++;
continue;
}
- if (aa.annotations[column].colour == null)
+ if (aa_annotations[column].colour == null)
g.setColor(Color.black);
else
g.setColor(Color.black);
else
- g.setColor(aa.annotations[column].colour);
+ g.setColor(aa_annotations[column].colour);
y1 = y
y1 = y
- - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
+ - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
y2 = y
y2 = y
- - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
+ - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
+ charWidth / 2, y2);
x++;
}
g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
+ charWidth / 2, y2);
x++;
}
- if (aa.threshold != null)
+ if (_aa.threshold != null)
{
{
- g.setColor(aa.threshold.colour);
+ 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));
Graphics2D g2 = (Graphics2D) g;
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) * charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+ public void drawBarGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
int eRes, float min, float max, int y)
{
int eRes, float min, float max, int y)
{
- if (sRes > aa.annotations.length)
+ if (sRes > aa_annotations.length)
{
return;
}
Font ofont = g.getFont();
{
return;
}
Font ofont = g.getFont();
- eRes = Math.min(eRes, aa.annotations.length);
+ eRes = Math.min(eRes, aa_annotations.length);
int x = 0, y1 = y, y2 = y;
int x = 0, y1 = y, y2 = y;
@@
-807,7
+808,7
@@
public class AnnotationRenderer
if (min < 0)
{
if (min < 0)
{
- y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
+ y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
}
g.setColor(Color.gray);
}
g.setColor(Color.gray);
@@
-815,16
+816,16
@@
public class AnnotationRenderer
g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
int column;
g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
int column;
- int aaMax = aa.annotations.length - 1;
+ int aaMax = aa_annotations.length - 1;
boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
// if (aa.autoCalculated && aa.label.startsWith("Consensus"))
{
// TODO: generalise this to have render styles for consensus/profile data
boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
// if (aa.autoCalculated && aa.label.startsWith("Consensus"))
{
// TODO: generalise this to have render styles for consensus/profile data
- if (aa.groupRef != null)
+ if (_aa.groupRef != null)
{
{
- renderHistogram = aa.groupRef.isShowConsensusHistogram();
- renderProfile = aa.groupRef.isShowSequenceLogo();
- normaliseProfile = aa.groupRef.isNormaliseSequenceLogo();
+ renderHistogram = _aa.groupRef.isShowConsensusHistogram();
+ renderProfile = _aa.groupRef.isShowSequenceLogo();
+ normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo();
}
else
{
}
else
{
@@
-846,18
+847,18
@@
public class AnnotationRenderer
break;
}
break;
}
- if (aa.annotations[column] == null)
+ if (aa_annotations[column] == null)
{
x++;
continue;
}
{
x++;
continue;
}
- if (aa.annotations[column].colour == null)
+ if (aa_annotations[column].colour == null)
g.setColor(Color.black);
else
g.setColor(Color.black);
else
- g.setColor(aa.annotations[column].colour);
+ g.setColor(aa_annotations[column].colour);
y1 = y
y1 = y
- - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
+ - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
if (renderHistogram)
{
if (renderHistogram)
{
@@
-874,12
+875,12
@@
public class AnnotationRenderer
if (renderProfile)
{
if (renderProfile)
{
- int profl[] = getProfileFor(aa, column);
+ int profl[] = getProfileFor(_aa, column);
// just try to draw the logo if profl is not null
if (profl != null && profl[1] != 0)
{
// just try to draw the logo if profl is not null
if (profl != null && profl[1] != 0)
{
- float ht = normaliseProfile ? y - aa.graphHeight : y1;
- double htn = normaliseProfile ? aa.graphHeight : (y2 - y1);// aa.graphHeight;
+ float ht = normaliseProfile ? y - _aa.graphHeight : y1;
+ double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
double hght;
float wdth;
double ht2 = 0;
double hght;
float wdth;
double ht2 = 0;
@@
-906,17
+907,17
@@
public class AnnotationRenderer
{
dc[0] = (char) profl[c++];
{
dc[0] = (char) profl[c++];
- if (aa.label.startsWith("StrucConsensus"))
+ if (_aa.label.startsWith("StrucConsensus"))
{
dc[1] = (char) profl[c++];
}
wdth = charWidth;
{
dc[1] = (char) profl[c++];
}
wdth = charWidth;
- wdth /= (float) fm.charsWidth(dc, 0, dc.length);
+ wdth /= fm.charsWidth(dc, 0, dc.length);
ht += scl;
{
ht += scl;
{
- scl = ((double) htn) * scale * ((double) profl[c++]);
+ scl = htn * scale * profl[c++];
lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
.getFontRenderContext());
g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
.getFontRenderContext());
g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
@@
-941,25
+942,25
@@
public class AnnotationRenderer
}
x++;
}
}
x++;
}
- if (aa.threshold != null)
+ if (_aa.threshold != null)
{
{
- g.setColor(aa.threshold.colour);
+ 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));
Graphics2D g2 = (Graphics2D) g;
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) * charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
// used by overview window
g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
// used by overview window
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
+ public void drawGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int width,
int y, int sRes, int eRes)
{
int y, int sRes, int eRes)
{
- eRes = Math.min(eRes, aa.annotations.length);
+ eRes = Math.min(eRes, aa_annotations.length);
g.setColor(Color.white);
g.fillRect(0, 0, width, y);
g.setColor(new Color(0, 0, 180));
g.setColor(Color.white);
g.fillRect(0, 0, width, y);
g.setColor(new Color(0, 0, 180));
@@
-968,14
+969,14
@@
public class AnnotationRenderer
for (int j = sRes; j < eRes; j++)
{
for (int j = sRes; j < eRes; j++)
{
- if (aa.annotations[j] != null)
+ if (aa_annotations[j] != null)
{
{
- if (aa.annotations[j].colour == null)
+ if (aa_annotations[j].colour == null)
g.setColor(Color.black);
else
g.setColor(Color.black);
else
- g.setColor(aa.annotations[j].colour);
+ 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;
if (height > y)
{
height = y;