X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=c1b1ab21250b9d210e8a064b228c03d41ffb8171;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=64ab8594fee1b31cbb62f95eba831eac020d6bbd;hpb=ac1d5169b86af13d4f06152a09cb125309ddf76f;p=jalview.git
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 64ab859..c1b1ab2 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -1,29 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview 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 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
* 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
import jalview.analysis.AAFrequency;
+import jalview.analysis.CodingUtils;
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.schemes.ResidueProperties;
import java.awt.BasicStroke;
import java.awt.Color;
@@ -35,16 +40,39 @@ import java.awt.Image;
import java.awt.font.LineMetrics;
import java.awt.geom.AffineTransform;
import java.awt.image.ImageObserver;
+import java.util.BitSet;
import java.util.Hashtable;
import com.stevesoft.pat.Regex;
public class AnnotationRenderer
{
+ private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
+
+ private static final int CHAR_A = 'A'; // 65
+
+ private static final int CHAR_Z = 'Z'; // 90
+
+ /**
+ * flag indicating if timing and redraw parameter info should be output
+ */
+ private final boolean debugRedraw;
public AnnotationRenderer()
{
- // TODO Auto-generated constructor stub
+ this(false);
+ }
+
+ /**
+ * Create a new annotation Renderer
+ *
+ * @param debugRedraw
+ * flag indicating if timing and redraw parameter info should be
+ * output
+ */
+ public AnnotationRenderer(boolean debugRedraw)
+ {
+ this.debugRedraw = debugRedraw;
}
public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
@@ -57,26 +85,26 @@ public class AnnotationRenderer
int x2 = (x * charWidth);
Regex closeparen = new Regex("(\\))");
- String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
- : row_annotations[column - 1].displayCharacter;
+ char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
+ : row_annotations[column - 1].secondaryStructure;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+ || dc != row_annotations[sCol - 1].secondaryStructure;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
- || !dc.equals(row_annotations[column].displayCharacter);
+ || dc != row_annotations[column].secondaryStructure;
// 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 (column > 0 && ResidueProperties.isCloseParenRNA(dc))
{
-
+
if (diffupstream)
// 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[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+ new int[] { y + iconOffset, y + 14 + iconOffset,
+ y + 8 + iconOffset }, 3);
x1 += 5;
}
if (diffdownstream)
@@ -86,13 +114,12 @@ public class AnnotationRenderer
}
else
{
-
+
// display a forward arrow
if (diffdownstream)
{
- g.fillPolygon(new int[]
- { x2 - 5, x2 - 5, x2 }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
+ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
x2 -= 5;
}
if (diffupstream)
@@ -110,7 +137,7 @@ public class AnnotationRenderer
private FontMetrics fm;
- private final boolean MAC = new jalview.util.Platform().isAMac();
+ private final boolean MAC = jalview.util.Platform.isAMac();
boolean av_renderHistogram = true, av_renderProfile = true,
av_normaliseProfile = false;
@@ -121,6 +148,8 @@ public class AnnotationRenderer
private Hashtable[] hconsensus;
+ private Hashtable[] complementConsensus;
+
private Hashtable[] hStrucConsensus;
private boolean av_ignoreGapsConsensus;
@@ -144,19 +173,41 @@ public class AnnotationRenderer
*/
private int imgWidth;
-
- public void drawPseudoNode(Graphics g, Color nonCanColor, Annotation[] row_annotations,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
+ /**
+ * offset to beginning of visible area
+ */
+ private int sOffset;
+
+ /**
+ * offset to end of visible area
+ */
+ private int visHeight;
+
+ /**
+ * indicate if the renderer should only render the visible portion of the
+ * annotation given the current view settings
+ */
+ private boolean useClip = true;
+
+ /**
+ * master flag indicating if renderer should ever try to clip. not enabled for
+ * jalview 2.8.1
+ */
+ private boolean canClip = false;
+
+ public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
+ Annotation[] row_annotations, int lastSSX, int x, int y,
+ int iconOffset, int startRes, int column, boolean validRes,
+ boolean validEnd)
{
- //System.out.println(nonCanColor);
-
+ // System.out.println(nonCanColor);
+
g.setColor(nonCanColor);
int sCol = (lastSSX / charWidth) + startRes;
int x1 = lastSSX;
int x2 = (x * charWidth);
Regex closeparen = new Regex("}|]|<|[a-z]");
-
+
String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
: row_annotations[column - 1].displayCharacter;
@@ -167,16 +218,17 @@ public class AnnotationRenderer
|| !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))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc)) )
+ if (column > 0 && closeparen.search(dc))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc))
+ // )
{
-
+
if (diffupstream)
// 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[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+ new int[] { y + iconOffset, y + 14 + iconOffset,
+ y + 8 + iconOffset }, 3);
x1 += 5;
}
if (diffdownstream)
@@ -186,13 +238,12 @@ public class AnnotationRenderer
}
else
{
-
+
// display a forward arrow
if (diffdownstream)
{
- g.fillPolygon(new int[]
- { x2 - 5, x2 - 5, x2 }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
+ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
x2 -= 5;
}
if (diffupstream)
@@ -203,6 +254,7 @@ public class AnnotationRenderer
// draw arrow body
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
}
+
// public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
// av)
public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
@@ -212,6 +264,26 @@ public class AnnotationRenderer
annotationPanel = annotPanel;
fadedImage = annotPanel.getFadedImage();
imgWidth = annotPanel.getFadedImageWidth();
+ // visible area for rendering
+ int[] bounds = annotPanel.getVisibleVRange();
+ if (bounds != null)
+ {
+ sOffset = bounds[0];
+ visHeight = bounds[1];
+ if (visHeight == 0)
+ {
+ useClip = false;
+ }
+ else
+ {
+ useClip = canClip;
+ }
+ }
+ else
+ {
+ useClip = false;
+ }
+
updateFromAlignViewport(av);
}
@@ -234,32 +306,54 @@ public class AnnotationRenderer
: new jalview.schemes.ZappoColourScheme();
}
columnSelection = av.getColumnSelection();
- hconsensus = av.getSequenceConsensusHash();// hconsensus;
- hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus;
- av_ignoreGapsConsensus = av.getIgnoreGapsConsensus();
+ hconsensus = av.getSequenceConsensusHash();
+ complementConsensus = av.getComplementConsensusHash();
+ hStrucConsensus = av.getRnaStructureConsensusHash();
+ av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
}
+ /**
+ * Returns profile data; the first element is the profile type, the second is
+ * the number of distinct values, the third the total count, and the remainder
+ * depend on the profile type.
+ *
+ * @param aa
+ * @param column
+ * @return
+ */
public int[] getProfileFor(AlignmentAnnotation aa, int column)
{
// TODO : consider refactoring the global alignment calculation
// properties/rendering attributes as a global 'alignment group' which holds
// all vis settings for the alignment as a whole rather than a subset
//
- if (aa.autoCalculated && aa.label.startsWith("Consensus"))
+ if (aa.autoCalculated
+ && (aa.label.startsWith("Consensus") || aa.label
+ .startsWith("cDNA Consensus")))
{
+ boolean forComplement = aa.label.startsWith("cDNA Consensus");
if (aa.groupRef != null && aa.groupRef.consensusData != null
&& aa.groupRef.isShowSequenceLogo())
{
+ // TODO? group consensus for cDNA complement
return AAFrequency.extractProfile(
aa.groupRef.consensusData[column],
aa.groupRef.getIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to
// be stored
- if (aa.groupRef == null && aa.sequenceRef == null && av_renderProfile)
+ if (aa.groupRef == null && aa.sequenceRef == null)
{
- return AAFrequency.extractProfile(hconsensus[column],
- av_ignoreGapsConsensus);
+ if (forComplement)
+ {
+ return AAFrequency.extractCdnaProfile(
+ complementConsensus[column], av_ignoreGapsConsensus);
+ }
+ else
+ {
+ return AAFrequency.extractProfile(hconsensus[column],
+ av_ignoreGapsConsensus);
+ }
}
}
else
@@ -278,7 +372,7 @@ public class AnnotationRenderer
// to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
- && av_renderProfile && hStrucConsensus != null
+ && hStrucConsensus != null
&& hStrucConsensus.length > column)
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
@@ -289,6 +383,8 @@ public class AnnotationRenderer
return null;
}
+ boolean rna = false;
+
/**
* Render the annotation rows associated with an alignment.
*
@@ -311,6 +407,7 @@ public class AnnotationRenderer
AlignViewportI av, Graphics g, int activeRow, int startRes,
int endRes)
{
+ long stime = System.currentTimeMillis();
boolean usedFaded = false;
// NOTES:
// AnnotationPanel needs to implement: ImageObserver, access to
@@ -319,7 +416,7 @@ public class AnnotationRenderer
fm = g.getFontMetrics();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int temp = 0;
- if (aa==null)
+ if (aa == null)
{
return false;
}
@@ -331,18 +428,55 @@ public class AnnotationRenderer
boolean validRes = false;
boolean validEnd = false;
boolean labelAllCols = false;
- boolean centreColLabels, centreColLabelsDef = av
- .getCentreColumnLabels();
+ boolean centreColLabels;
+ boolean centreColLabelsDef = av.isCentreColumnLabels();
boolean scaleColLabel = false;
- boolean[] graphGroupDrawn = new boolean[aa.length];
+ final AlignmentAnnotation consensusAnnot = av
+ .getAlignmentConsensusAnnotation();
+ final AlignmentAnnotation structConsensusAnnot = av
+ .getAlignmentStrucConsensusAnnotation();
+ final AlignmentAnnotation complementConsensusAnnot = av
+ .getComplementConsensusAnnotation();
+ boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
+
+ BitSet graphGroupDrawn = new BitSet();
int charOffset = 0; // offset for a label
float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
// column.
Font ofont = g.getFont();
// \u03B2 \u03B1
+ // debug ints
+ int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
+ boolean clipst = false, clipend = false;
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
+ isRNA = row.isRNA();
+ {
+ // check if this is a consensus annotation row and set the display
+ // settings appropriately
+ // TODO: generalise this to have render styles for consensus/profile
+ // data
+ if (row.groupRef != null && row == row.groupRef.getConsensus())
+ {
+ renderHistogram = row.groupRef.isShowConsensusHistogram();
+ renderProfile = row.groupRef.isShowSequenceLogo();
+ normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
+ }
+ else if (row == consensusAnnot || row == structConsensusAnnot
+ || row == complementConsensusAnnot)
+ {
+ renderHistogram = av_renderHistogram;
+ renderProfile = av_renderProfile;
+ normaliseProfile = av_normaliseProfile;
+ }
+ else
+ {
+ renderHistogram = true;
+ // don't need to set render/normaliseProfile since they are not
+ // currently used in any other annotation track renderer
+ }
+ }
Annotation[] row_annotations = row.annotations;
if (!row.visible)
{
@@ -353,132 +487,151 @@ public class AnnotationRenderer
scaleColLabel = row.scaleColLabel;
lastSS = ' ';
lastSSX = 0;
- if (row.graph > 0)
- {
- if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
- {
- continue;
- }
-
- // this is so that we draw the characters below the graph
- y += row.height;
- if (row.hasText)
+ if (!useClip
+ || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
+ {// if_in_visible_region
+ if (!clipst)
{
- iconOffset = charHeight - fm.getDescent();
- y -= charHeight;
+ clipst = true;
+ yfrom = y;
+ f_i = i;
}
- }
- else if (row.hasText)
- {
- iconOffset = charHeight - fm.getDescent();
-
- }
- else
- {
- iconOffset = 0;
- }
+ yto = y;
+ f_to = i;
+ if (row.graph > 0)
+ {
+ if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
+ {
+ continue;
+ }
- if (row.autoCalculated && av.isCalculationInProgress(row))
- {
- y += charHeight;
- usedFaded = true;
- g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
- - row.height, imgWidth, y, annotationPanel);
- g.setColor(Color.black);
- // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
+ // this is so that we draw the characters below the graph
+ y += row.height;
- continue;
- }
-
- /*
- * else if (annotationPanel.av.updatingConservation &&
- * aa[i].label.equals("Conservation")) {
- *
- * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
- * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
- * annotationPanel.imgWidth, y, annotationPanel);
- *
- * g.setColor(Color.black); //
- * g.drawString("Calculating Conservation.....",20, y-row.height/2);
- *
- * continue; } else if (annotationPanel.av.updatingConservation &&
- * aa[i].label.equals("Quality")) {
- *
- * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
- * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
- * annotationPanel.imgWidth, y, annotationPanel); g.setColor(Color.black);
- * // / g.drawString("Calculating Quality....",20, y-row.height/2);
- *
- * continue; }
- */
- // first pass sets up state for drawing continuation from left-hand column
- // of startRes
- x = (startRes == 0) ? 0 : -1;
- while (x < endRes - startRes)
- {
- if (hasHiddenColumns)
- {
- column = columnSelection.adjustForHiddenColumns(startRes + x);
- if (column > row_annotations.length - 1)
+ if (row.hasText)
{
- break;
+ iconOffset = charHeight - fm.getDescent();
+ y -= charHeight;
}
}
- else
+ else if (row.hasText)
{
- column = startRes + x;
- }
+ iconOffset = charHeight - fm.getDescent();
- if ((row_annotations == null) || (row_annotations.length <= column)
- || (row_annotations[column] == null))
- {
- validRes = false;
}
else
{
- validRes = true;
+ iconOffset = 0;
}
- if (x > -1)
+
+ if (row.autoCalculated && av.isCalculationInProgress(row))
{
- if (activeRow == i)
- {
- g.setColor(Color.red);
+ y += charHeight;
+ usedFaded = true;
+ g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
+ - row.height, imgWidth, y, annotationPanel);
+ g.setColor(Color.black);
+ // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
- if (columnSelection != null)
- {
- for (int n = 0; n < columnSelection.size(); n++)
- {
- int v = columnSelection.columnAt(n);
+ continue;
+ }
- if (v == column)
- {
- g.fillRect(x * charWidth, y, charWidth, charHeight);
- }
- }
+ /*
+ * else if (annotationPanel.av.updatingConservation &&
+ * aa[i].label.equals("Conservation")) {
+ *
+ * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
+ * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
+ * annotationPanel.imgWidth, y, annotationPanel);
+ *
+ * g.setColor(Color.black); //
+ * g.drawString("Calculating Conservation.....",20, y-row.height/2);
+ *
+ * continue; } else if (annotationPanel.av.updatingConservation &&
+ * aa[i].label.equals("Quality")) {
+ *
+ * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
+ * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
+ * annotationPanel.imgWidth, y, annotationPanel);
+ * g.setColor(Color.black); // /
+ * g.drawString("Calculating Quality....",20, y-row.height/2);
+ *
+ * continue; }
+ */
+ // first pass sets up state for drawing continuation from left-hand
+ // column
+ // of startRes
+ x = (startRes == 0) ? 0 : -1;
+ while (x < endRes - startRes)
+ {
+ if (hasHiddenColumns)
+ {
+ column = columnSelection.adjustForHiddenColumns(startRes + x);
+ if (column > row_annotations.length - 1)
+ {
+ break;
}
}
- if (!row.isValidStruc())
+ else
+ {
+ column = startRes + x;
+ }
+
+ if ((row_annotations == null)
+ || (row_annotations.length <= column)
+ || (row_annotations[column] == null))
+ {
+ validRes = false;
+ }
+ else
{
- g.setColor(Color.orange);
- g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
- charWidth, charHeight);
+ validRes = true;
}
- if (validCharWidth
- && validRes
- && row_annotations[column].displayCharacter != null
- && (row_annotations[column].displayCharacter.length() > 0))
+ final String displayChar = validRes ? row_annotations[column].displayCharacter
+ : null;
+ if (x > -1)
{
+ if (activeRow == i)
+ {
+ g.setColor(Color.red);
+
+ if (columnSelection != null)
+ {
+ for (int n = 0; n < columnSelection.size(); n++)
+ {
+ int v = columnSelection.columnAt(n);
- if (centreColLabels || scaleColLabel)
+ if (v == column)
+ {
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
+ }
+ }
+ }
+ }
+ if (row.getInvalidStrucPos() > x)
+ {
+ g.setColor(Color.orange);
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
+ }
+ else if (row.getInvalidStrucPos() == x)
+ {
+ g.setColor(Color.orange.darker());
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
+ }
+ if (validCharWidth && validRes && displayChar != null
+ && (displayChar.length() > 0))
{
- fmWidth = fm.charsWidth(
- row_annotations[column].displayCharacter
- .toCharArray(), 0,
- row_annotations[column].displayCharacter.length());
- if (scaleColLabel)
+ fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
+ displayChar.length());
+ if (/* centreColLabels || */scaleColLabel)
{
+ // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
+ // displayChar.length());
+ //
+ // if (scaleColLabel)
+ // {
// justify the label and scale to fit in column
if (fmWidth > charWidth)
{
@@ -490,382 +643,393 @@ public class AnnotationRenderer
// and update the label's width to reflect the scaling.
fmWidth = charWidth;
}
+ // }
+ }
+ // TODO is it ok to use width of / show all characters here?
+ // else
+ // {
+ // fmWidth = fm.charWidth(displayChar.charAt(0));
+ // }
+ charOffset = (int) ((charWidth - fmWidth) / 2f);
+
+ if (row_annotations[column].colour == null)
+ {
+ g.setColor(Color.black);
+ }
+ else
+ {
+ g.setColor(row_annotations[column].colour);
}
- }
- else
- {
- fmWidth = fm
- .charWidth(row_annotations[column].displayCharacter
- .charAt(0));
- }
- charOffset = (int) ((charWidth - fmWidth) / 2f);
-
- if (row_annotations[column].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(row_annotations[column].colour);
- if (column == 0 || row.graph > 0)
- {
- g.drawString(row_annotations[column].displayCharacter,
- (x * charWidth) + charOffset, y + iconOffset);
- }
- else if (row_annotations[column - 1] == null
- || (labelAllCols
- || !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
- * charWidth + charOffset, y + iconOffset);
+ if (column == 0 || row.graph > 0)
+ {
+ g.drawString(displayChar, (x * charWidth) + charOffset, y
+ + iconOffset);
+ }
+ else if (row_annotations[column - 1] == null
+ || (labelAllCols
+ || !displayChar
+ .equals(row_annotations[column - 1].displayCharacter) || (displayChar
+ .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
+ {
+ g.drawString(displayChar, x * charWidth + charOffset, y
+ + iconOffset);
+ }
+ g.setFont(ofont);
}
- g.setFont(ofont);
}
- }
- if (row.hasIcons)
- {
- char ss = validRes ? row_annotations[column].secondaryStructure
- : '-';
-
- if (ss == '(')
+ if (row.hasIcons)
{
- // distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf(')') > -1)
+ char ss = validRes ? row_annotations[column].secondaryStructure
+ : '-';
+
+ if (ss == '(')
{
-
- ss = ')';
-
+ // distinguish between forward/backward base-pairing
+ if (displayChar.indexOf(')') > -1)
+ {
+
+ ss = ')';
+
+ }
}
- }
- if (ss == '[')
- {
- if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
+ if (ss == '[')
{
+ if ((displayChar.indexOf(']') > -1))
+ {
ss = ']';
-
-
+
+ }
}
- }
- if (ss == '{')
- {
- // distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf('}') > -1)
- {
- ss = '}';
-
-
- }
- }
- if (ss == '<')
- {
- // distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf('<') > -1)
- {
- ss = '>';
-
-
- }
- }
- if (ss >=65)
- {
- // System.out.println("ss="+ss);
- // distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf(ss+32) > -1)
- {
-
- ss = (char) (ss+32);
-
-
- }
- }
-
-
- if (!validRes || (ss != lastSS))
- {
-
-
- if (x > -1)
+ if (ss == '{')
{
-
-
- int nb_annot=x-temp;
- //System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
- switch (lastSS)
+ // distinguish between forward/backward base-pairing
+ if (displayChar.indexOf('}') > -1)
{
-
- case '$':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- case 'µ':
- drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- case '(': // Stem case for RNA secondary structure
- case ')': // and opposite direction
-
-
- drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- temp=x;
- break;
- case '{':
- case '}':
- case '[':
- case ']':
- case '>':
- case '<':
- case 'A':
- case 'a':
- case 'B':
- case 'b':
- case 'C':
- case 'c':
- case 'D':
- case 'd':
- case 'E':
- case 'e':
- case 'F':
- case 'f':
- case 'G':
- case 'g':
- case 'H':
- case 'h':
- case 'I':
- case 'i':
- case 'J':
- case 'j':
- case 'K':
- case 'k':
- case 'L':
- case 'l':
- case 'M':
- case 'm':
- case 'N':
- case 'n':
- case 'O':
- case 'o':
- case 'P':
- case 'p':
- case 'Q':
- case 'q':
- case 'R':
- case 'r':
- case 'S':
- case 's':
- case 'T':
- case 't':
- case 'U':
- case 'u':
- case 'V':
- case 'v':
- case 'W':
- case 'w':
- case 'X':
- case 'x':
- case 'Y':
- case 'y':
- case 'Z':
- case 'z':
-
- Color nonCanColor= getNotCanonicalColor(lastSS);
- drawPseudoNode(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- temp=x;
- break;
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- - lastSSX, 2);
- temp=x;
- break;
+ ss = '}';
+
}
}
- if (validRes)
+ if (ss == '<')
{
- lastSS = ss;
+ // distinguish between forward/backward base-pairing
+ if (displayChar.indexOf('<') > -1)
+ {
+ ss = '>';
+
+ }
}
- else
+ if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
{
- lastSS = ' ';
+ // distinguish between forward/backward base-pairing
+ int ssLowerCase = ss + UPPER_TO_LOWER;
+ // TODO would .equals() be safer here? or charAt(0)?
+ if (displayChar.indexOf(ssLowerCase) > -1)
+ {
+ ss = (char) ssLowerCase;
+ }
}
- if (x > -1)
+
+ if (!validRes || (ss != lastSS))
{
- lastSSX = (x * charWidth);
+
+ if (x > -1)
+ {
+
+ int nb_annot = x - temp;
+ // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
+ switch (lastSS)
+ {
+ case '(': // Stem case for RNA secondary structure
+ case ')': // and opposite direction
+ drawStemAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes, validEnd);
+ temp = x;
+ break;
+
+ case 'H':
+ if (!isRNA)
+ {
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes,
+ validEnd);
+ break;
+ }
+
+ case 'E':
+ if (!isRNA)
+ {
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes,
+ validEnd);
+ break;
+ }
+
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
+ case 'c':
+ case 'D':
+ case 'd':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'S':
+ case 's':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+
+ Color nonCanColor = getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
+ lastSSX, x, y, iconOffset, startRes, column,
+ validRes, validEnd);
+ temp = x;
+ break;
+ default:
+ g.setColor(Color.gray);
+ g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
+ - lastSSX, 2);
+ temp = x;
+ break;
+ }
+ }
+ if (validRes)
+ {
+ lastSS = ss;
+ }
+ else
+ {
+ lastSS = ' ';
+ }
+ if (x > -1)
+ {
+ lastSSX = (x * charWidth);
+ }
}
}
+ column++;
+ x++;
+ }
+ if (column >= row_annotations.length)
+ {
+ column = row_annotations.length - 1;
+ validEnd = false;
+ }
+ else
+ {
+ validEnd = true;
+ }
+ if ((row_annotations == null) || (row_annotations.length <= column)
+ || (row_annotations[column] == null))
+ {
+ validRes = false;
+ }
+ else
+ {
+ validRes = true;
}
- column++;
- x++;
- }
- if (column >= row_annotations.length)
- {
- column = row_annotations.length - 1;
- validEnd = false;
- }
- else
- {
- validEnd = true;
- }
- if ((row_annotations == null) || (row_annotations.length <= column)
- || (row_annotations[column] == null))
- {
- validRes = false;
- }
- else
- {
- validRes = true;
- }
- // x ++;
+ // x ++;
- if (row.hasIcons)
- {
- switch (lastSS)
+ if (row.hasIcons)
{
- case '$':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- case 'µ':
- drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
- case 's':
- case 'S': // Stem case for RNA secondary structure
-
- drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
-
- break;
- case '{':
- case '}':
- case '[':
- case ']':
- case '>':
- case '<':
- case 'A':
- case 'a':
- case 'B':
- case 'b':
- case 'C':
- case 'c':
- case 'D':
- case 'd':
- case 'E':
- case 'e':
- case 'F':
- case 'f':
- case 'G':
- case 'g':
- case 'H':
- case 'h':
- case 'I':
- case 'i':
- case 'J':
- case 'j':
- case 'K':
- case 'k':
- case 'L':
- case 'l':
- case 'M':
- case 'm':
- case 'N':
- case 'n':
- case 'O':
- case 'o':
- case 'P':
- case 'p':
- case 'Q':
- case 'q':
- case 'R':
- case 'r':
- case 'T':
- case 't':
- case 'U':
- case 'u':
- case 'V':
- case 'v':
- case 'W':
- case 'w':
- case 'X':
- case 'x':
- case 'Y':
- case 'y':
- case 'Z':
- case 'z':
- //System.out.println(lastSS);
-
- Color nonCanColor = getNotCanonicalColor(lastSS);
- drawPseudoNode(g,nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
-
- break;
-
- default:
- drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
+ switch (lastSS)
+ {
+
+ case 'H':
+ if (!isRNA)
+ {
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
+ }
+
+ case 'E':
+ if (!isRNA)
+ {
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
+ }
+
+ case '(':
+ case ')': // Stem case for RNA secondary structure
+
+ drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+
+ break;
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
+ case 'c':
+ case 'D':
+ case 'd':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+ // System.out.println(lastSS);
+ Color nonCanColor = getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
+ x, y, iconOffset, startRes, column, validRes, validEnd);
+ break;
+ default:
+ drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
+ }
}
- }
- if (row.graph > 0 && row.graphHeight > 0)
- {
- if (row.graph == AlignmentAnnotation.LINE_GRAPH)
+ if (row.graph > 0 && row.graphHeight > 0)
{
- if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
+ if (row.graph == AlignmentAnnotation.LINE_GRAPH)
{
- float groupmax = -999999, groupmin = 9999999;
- for (int gg = 0; gg < aa.length; gg++)
+ if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
{
- if (aa[gg].graphGroup != row.graphGroup)
+ // TODO: JAL-1291 revise rendering model so the graphGroup map is
+ // computed efficiently for all visible labels
+ float groupmax = -999999, groupmin = 9999999;
+ for (int gg = 0; gg < aa.length; gg++)
{
- continue;
- }
+ if (aa[gg].graphGroup != row.graphGroup)
+ {
+ continue;
+ }
- if (aa[gg] != row)
- {
- aa[gg].visible = false;
+ if (aa[gg] != row)
+ {
+ aa[gg].visible = false;
+ }
+ if (aa[gg].graphMax > groupmax)
+ {
+ groupmax = aa[gg].graphMax;
+ }
+ if (aa[gg].graphMin < groupmin)
+ {
+ groupmin = aa[gg].graphMin;
+ }
}
- if (aa[gg].graphMax > groupmax)
- {
- groupmax = aa[gg].graphMax;
- }
- if (aa[gg].graphMin < groupmin)
+ for (int gg = 0; gg < aa.length; gg++)
{
- groupmin = aa[gg].graphMin;
+ if (aa[gg].graphGroup == row.graphGroup)
+ {
+ drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
+ endRes, y, groupmin, groupmax, row.graphHeight);
+ }
}
- }
- for (int gg = 0; gg < aa.length; gg++)
+ graphGroupDrawn.set(row.graphGroup);
+ }
+ else
{
- if (aa[gg].graphGroup == row.graphGroup)
- {
- drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin,
- groupmax, row.graphHeight);
- }
+ drawLineGraph(g, row, row_annotations, startRes, endRes, y,
+ row.graphMin, row.graphMax, row.graphHeight);
}
-
- graphGroupDrawn[row.graphGroup] = true;
}
- else
+ else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
- drawLineGraph(g, row, row_annotations, startRes, endRes, y, row.graphMin,
- row.graphMax, row.graphHeight);
+ drawBarGraph(g, row, row_annotations, startRes, endRes,
+ row.graphMin, row.graphMax, y, renderHistogram,
+ renderProfile, normaliseProfile);
}
}
- else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
+ }
+ else
+ {
+ if (clipst && !clipend)
{
- drawBarGraph(g, row, row_annotations, startRes, endRes, row.graphMin,
- row.graphMax, y);
+ clipend = true;
}
- }
-
+ }// end if_in_visible_region
if (row.graph > 0 && row.hasText)
{
y += charHeight;
@@ -876,22 +1040,43 @@ public class AnnotationRenderer
y += aa[i].height;
}
}
+ if (debugRedraw)
+ {
+ if (canClip)
+ {
+ if (clipst)
+ {
+ System.err.println("Start clip at : " + yfrom + " (index " + f_i
+ + ")");
+ }
+ if (clipend)
+ {
+ System.err.println("End clip at : " + yto + " (index " + f_to
+ + ")");
+ }
+ }
+ ;
+ System.err.println("Annotation Rendering time:"
+ + (System.currentTimeMillis() - stime));
+ }
+ ;
+
return !usedFaded;
}
- private final Color GLYPHLINE_COLOR = Color.gray;
+ public static final Color GLYPHLINE_COLOR = Color.gray;
- private final Color SHEET_COLOUR = Color.green;
+ public static final Color SHEET_COLOUR = Color.green;
- private final Color HELIX_COLOUR = Color.red;
+ public static final Color HELIX_COLOUR = Color.red;
- private final Color STEM_COLOUR = Color.blue;
-
- private Color sdNOTCANONICAL_COLOUR;
+ public static final Color STEM_COLOUR = Color.blue;
- public void drawGlyphLine(Graphics g, Annotation[] row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
+ private Color sdNOTCANONICAL_COLOUR;
+
+ public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
+ int x, int y, int iconOffset, int startRes, int column,
+ boolean validRes, boolean validEnd)
{
g.setColor(GLYPHLINE_COLOR);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
@@ -899,8 +1084,8 @@ public class AnnotationRenderer
public void drawSheetAnnot(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)
{
g.setColor(SHEET_COLOUR);
@@ -909,11 +1094,9 @@ public class AnnotationRenderer
{
g.fillRect(lastSSX, y + 4 + iconOffset,
(x * charWidth) - lastSSX - 4, 7);
- g.fillPolygon(new int[]
- { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
- new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
- 3);
+ g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
+ (x * charWidth) }, new int[] { y + iconOffset,
+ y + 14 + iconOffset, y + 7 + iconOffset }, 3);
}
else
{
@@ -1045,9 +1228,13 @@ public class AnnotationRenderer
}
if (aa_annotations[column].colour == null)
+ {
g.setColor(Color.black);
+ }
else
+ {
g.setColor(aa_annotations[column].colour);
+ }
y1 = y
- (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
@@ -1064,8 +1251,7 @@ public class AnnotationRenderer
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));
+ BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
@@ -1075,7 +1261,8 @@ public class AnnotationRenderer
public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int sRes, int eRes, float min,
- float max, int y)
+ float max, int y, boolean renderHistogram, boolean renderProfile,
+ boolean normaliseProfile)
{
if (sRes > aa_annotations.length)
{
@@ -1099,23 +1286,6 @@ public class AnnotationRenderer
int column;
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
- if (_aa.groupRef != null)
- {
- renderHistogram = _aa.groupRef.isShowConsensusHistogram();
- renderProfile = _aa.groupRef.isShowSequenceLogo();
- normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo();
- }
- else
- {
- renderHistogram = av_renderHistogram;
- renderProfile = av_renderProfile;
- normaliseProfile = av_normaliseProfile;
- }
- }
while (x < eRes - sRes)
{
column = sRes + x;
@@ -1135,9 +1305,13 @@ public class AnnotationRenderer
continue;
}
if (aa_annotations[column].colour == null)
+ {
g.setColor(Color.black);
+ }
else
+ {
g.setColor(aa_annotations[column].colour);
+ }
y1 = y
- (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
@@ -1157,10 +1331,16 @@ public class AnnotationRenderer
if (renderProfile)
{
+ /*
+ * {profile type, #values, total count, char1, pct1, char2, pct2...}
+ */
int profl[] = getProfileFor(_aa, column);
+
// just try to draw the logo if profl is not null
- if (profl != null && profl[1] != 0)
+ if (profl != null && profl[2] != 0)
{
+ boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
+ boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
float ht = normaliseProfile ? y - _aa.graphHeight : y1;
double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
double hght;
@@ -1169,55 +1349,80 @@ public class AnnotationRenderer
char[] dc;
/**
- * profl.length == 74 indicates that the profile of a secondary
- * structure conservation row was accesed. Therefore dc gets length 2,
- * to have space for a basepair instead of just a single nucleotide
+ * Render a single base for a sequence profile, a base pair for
+ * structure profile, and a triplet for a cdna profile
*/
- if (profl.length == 74)
- {
- dc = new char[2];
- }
- else
- {
- dc = new char[1];
- }
+ dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
+
LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
- double scale = 1f / (normaliseProfile ? profl[1] : 100f);
+ double scale = 1f / (normaliseProfile ? profl[2] : 100f);
float ofontHeight = 1f / lm.getAscent();// magnify to fill box
double scl = 0.0;
- for (int c = 2; c < profl[0];)
- {
- dc[0] = (char) profl[c++];
- if (_aa.label.startsWith("StrucConsensus"))
+ /*
+ * Traverse the character(s)/percentage data in the array
+ */
+ int c = 3;
+ int valuesProcessed = 0;
+ // profl[1] is the number of values in the profile
+ while (valuesProcessed < profl[1])
+ {
+ if (isStructureProfile)
{
+ // todo can we encode a structure pair as an int, like codons?
+ dc[0] = (char) profl[c++];
dc[1] = (char) profl[c++];
}
+ else if (isCdnaProfile)
+ {
+ dc = CodingUtils.decodeCodon(profl[c++]);
+ }
+ else
+ {
+ dc[0] = (char) profl[c++];
+ }
wdth = charWidth;
wdth /= fm.charsWidth(dc, 0, dc.length);
ht += scl;
+ // next profl[] position is profile % for the character(s)
+ scl = htn * scale * profl[c++];
+ lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
+ .getFontRenderContext());
+ g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
+ wdth, scl / lm.getAscent())));
+ lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
+
+ // Debug - render boxes around characters
+ // g.setColor(Color.red);
+ // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
+ // (int)(scl));
+ // g.setColor(profcolour.findColour(dc[0]).darker());
+
+ /*
+ * Set character colour as per alignment colour scheme; use the
+ * codon translation if a cDNA profile
+ */
+ Color colour = null;
+ if (isCdnaProfile)
+ {
+ final String codonTranslation = ResidueProperties
+ .codonTranslate(new String(dc));
+ colour = profcolour.findColour(codonTranslation.charAt(0),
+ column, null);
+ }
+ else
{
- scl = htn * scale * profl[c++];
- lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
- .getFontRenderContext());
- g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
- wdth, scl / lm.getAscent())));
- lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
-
- // Debug - render boxes around characters
- // g.setColor(Color.red);
- // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
- // (int)(scl));
- // g.setColor(profcolour.findColour(dc[0]).darker());
- g.setColor(profcolour.findColour(dc[0], column, null));
-
- hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
- .getBaselineIndex()]));
-
- g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
+ colour = profcolour.findColour(dc[0], column, null);
}
+ g.setColor(colour == Color.white ? Color.lightGray : colour);
+
+ hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
+ .getBaselineIndex()]));
+
+ g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
+ valuesProcessed++;
}
g.setFont(ofont);
}
@@ -1229,8 +1434,7 @@ public class AnnotationRenderer
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));
+ BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
y2 = (int) (y - ((_aa.threshold.value - min) / range)
* _aa.graphHeight);
@@ -1255,9 +1459,13 @@ public class AnnotationRenderer
if (aa_annotations[j] != null)
{
if (aa_annotations[j].colour == null)
+ {
g.setColor(Color.black);
+ }
else
+ {
g.setColor(aa_annotations[j].colour);
+ }
height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
if (height > y)
@@ -1271,134 +1479,130 @@ public class AnnotationRenderer
}
}
-
Color getNotCanonicalColor(char lastss)
- {
- switch (lastss)
- {
- case '{':
- case '}':
- return new Color(255,125,5);
-
- case '[':
- case ']':
- return new Color(245,115,10);
-
- case '>':
- case '<':
- return new Color(235,135,15);
-
- case 'A':
- case 'a':
- return new Color(225,105,20);
-
- case 'B':
- case 'b':
- return new Color(215,145,30);
-
- case 'C':
- case 'c':
- return new Color(205,95,35);
-
- case 'D':
- case 'd':
- return new Color(195,155,45);
-
- case 'E':
- case 'e':
- return new Color(185,85,55);
-
- case 'F':
- case 'f':
- return new Color(175,165,65);
-
- case 'G':
- case 'g':
- return new Color(170,75,75);
-
- case 'H':
- case 'h':
- return new Color(160,175,85);
-
- case 'I':
- case 'i':
- return new Color(150,65,95);
-
- case 'J':
- case 'j':
- return new Color(140,185,105);
-
- case 'K':
- case 'k':
- return new Color(130,55,110);
-
- case 'L':
- case 'l':
- return new Color(120,195,120);
-
- case 'M':
- case 'm':
- return new Color(110,45,130);
-
- case 'N':
- case 'n':
- return new Color(100,205,140);
-
- case 'O':
- case 'o':
- return new Color(90,35,150);
-
- case 'P':
- case 'p':
- return new Color(85,215,160);
-
- case 'Q':
- case 'q':
- return new Color(75,25,170);
-
- case 'R':
- case 'r':
- return new Color(65,225,180);
-
- case 'S':
- case 's':
- return new Color(55,15,185);
-
- case 'T':
- case 't':
- return new Color(45,235,195);
-
- case 'U':
- case 'u':
- return new Color(35,5,205);
-
- case 'V':
- case 'v':
- return new Color(25,245,215);
-
- case 'W':
- case 'w':
- return new Color(15,0,225);
-
- case 'X':
- case 'x':
- return new Color(10,255,235);
-
- case 'Y':
- case 'y':
- return new Color(5,150,245);
-
- case 'Z':
- case 'z':
- return new Color(0,80,255);
-
- default :
- System.out.println("This is not a interaction : "+lastss);
- return null;
-
- }
- }
-}
+ {
+ switch (lastss)
+ {
+ case '{':
+ case '}':
+ return new Color(255, 125, 5);
+
+ case '[':
+ case ']':
+ return new Color(245, 115, 10);
+
+ case '>':
+ case '<':
+ return new Color(235, 135, 15);
+
+ case 'A':
+ case 'a':
+ return new Color(225, 105, 20);
+
+ case 'B':
+ case 'b':
+ return new Color(215, 145, 30);
+
+ case 'C':
+ case 'c':
+ return new Color(205, 95, 35);
+
+ case 'D':
+ case 'd':
+ return new Color(195, 155, 45);
+
+ case 'E':
+ case 'e':
+ return new Color(185, 85, 55);
+
+ case 'F':
+ case 'f':
+ return new Color(175, 165, 65);
+
+ case 'G':
+ case 'g':
+ return new Color(170, 75, 75);
+
+ case 'H':
+ case 'h':
+ return new Color(160, 175, 85);
+
+ case 'I':
+ case 'i':
+ return new Color(150, 65, 95);
-
-
+ case 'J':
+ case 'j':
+ return new Color(140, 185, 105);
+
+ case 'K':
+ case 'k':
+ return new Color(130, 55, 110);
+
+ case 'L':
+ case 'l':
+ return new Color(120, 195, 120);
+
+ case 'M':
+ case 'm':
+ return new Color(110, 45, 130);
+
+ case 'N':
+ case 'n':
+ return new Color(100, 205, 140);
+
+ case 'O':
+ case 'o':
+ return new Color(90, 35, 150);
+
+ case 'P':
+ case 'p':
+ return new Color(85, 215, 160);
+
+ case 'Q':
+ case 'q':
+ return new Color(75, 25, 170);
+
+ case 'R':
+ case 'r':
+ return new Color(65, 225, 180);
+
+ case 'S':
+ case 's':
+ return new Color(55, 15, 185);
+
+ case 'T':
+ case 't':
+ return new Color(45, 235, 195);
+
+ case 'U':
+ case 'u':
+ return new Color(35, 5, 205);
+
+ case 'V':
+ case 'v':
+ return new Color(25, 245, 215);
+
+ case 'W':
+ case 'w':
+ return new Color(15, 0, 225);
+
+ case 'X':
+ case 'x':
+ return new Color(10, 255, 235);
+
+ case 'Y':
+ case 'y':
+ return new Color(5, 150, 245);
+
+ case 'Z':
+ case 'z':
+ return new Color(0, 80, 255);
+
+ default:
+ System.out.println("This is not a interaction : " + lastss);
+ return null;
+
+ }
+ }
+}