X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=d951aba819ea80526609d64018fb32aee4bae552;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=0d7d4ca463dd7ea60438dbce7f4121fe6ea0751c;hpb=f51ad53a1437086e6deea02e4f8930078b92bfcc;p=jalview.git
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 0d7d4ca..d951aba 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -1,9 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.renderer;
import jalview.analysis.AAFrequency;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.schemes.ColourSchemeI;
@@ -17,41 +36,56 @@ 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
{
+ /**
+ * 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, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
+ public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
{
g.setColor(STEM_COLOUR);
int sCol = (lastSSX / charWidth) + startRes;
int x1 = lastSSX;
int x2 = (x * charWidth);
Regex closeparen = new Regex("(\\))");
-
- 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);
+
+ 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 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)
- // 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[]
@@ -81,42 +115,91 @@ public class AnnotationRenderer
// draw arrow body
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
}
- private int charWidth,endRes,charHeight;
+
+ private int charWidth, endRes, charHeight;
+
private boolean validCharWidth, hasHiddenColumns;
+
private FontMetrics fm;
- private boolean MAC=new jalview.util.Platform().isAMac();
- boolean av_renderHistogram = true, av_renderProfile = true, av_normaliseProfile=false;
- ColourSchemeI profcolour=null;
+
+ private final boolean MAC = new jalview.util.Platform().isAMac();
+
+ boolean av_renderHistogram = true, av_renderProfile = true,
+ av_normaliseProfile = false;
+
+ ColourSchemeI profcolour = null;
+
private ColumnSelection columnSelection;
+
private Hashtable[] hconsensus;
+
private Hashtable[] hStrucConsensus;
+
private boolean av_ignoreGapsConsensus;
-
+
/**
* attributes set from AwtRenderPanelI
*/
/**
- * old image used when data is currently being calculated and cannot be rendered
+ * old image used when data is currently being calculated and cannot be
+ * rendered
*/
private Image fadedImage;
+
/**
* panel being rendered into
*/
private ImageObserver annotationPanel;
+
/**
* width of image to render in panel
*/
- private int imgWidth;
+ private int imgWidth;
+ /**
+ * 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 updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI av)
- public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel, AlignViewportI av)
+ // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
+ // av)
+ public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
+ AlignViewportI av)
{
fm = annotPanel.getFontMetrics();
annotationPanel = annotPanel;
- fadedImage=annotPanel.getFadedImage();
- imgWidth=annotPanel.getFadedImageWidth();
+ 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);
}
+
public void updateFromAlignViewport(AlignViewportI av)
{
charWidth = av.getCharWidth();
@@ -126,37 +209,42 @@ public class AnnotationRenderer
validCharWidth = av.isValidCharWidth();
av_renderHistogram = av.isShowConsensusHistogram();
av_renderProfile = av.isShowSequenceLogo();
- av_normaliseProfile= av.isNormaliseSequenceLogo();
+ av_normaliseProfile = av.isNormaliseSequenceLogo();
profcolour = av.getGlobalColourScheme();
if (profcolour == null)
{
- // Set the default colour for sequence logo if the alignnent has no colourscheme set
- profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme() : new jalview.schemes.ZappoColourScheme();
+ // Set the default colour for sequence logo if the alignnent has no
+ // colourscheme set
+ profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
+ : new jalview.schemes.ZappoColourScheme();
}
columnSelection = av.getColumnSelection();
- hconsensus = av.getSequenceConsensusHash();//hconsensus;
- hStrucConsensus = av.getRnaStructureConsensusHash(); //hStrucConsensus;
- av_ignoreGapsConsensus=av.getIgnoreGapsConsensus();
+ hconsensus = av.getSequenceConsensusHash();// hconsensus;
+ hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus;
+ av_ignoreGapsConsensus = av.getIgnoreGapsConsensus();
}
+
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
- //
+ // 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.groupRef != null && aa.groupRef.consensusData != null
&& aa.groupRef.isShowSequenceLogo())
{
return AAFrequency.extractProfile(
- aa.groupRef.consensusData[column], aa.groupRef
- .getIgnoreGapsConsensus());
+ 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);
+ return AAFrequency.extractProfile(hconsensus[column],
+ av_ignoreGapsConsensus);
}
}
else
@@ -164,20 +252,19 @@ public class AnnotationRenderer
if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
{
// TODO implement group structure consensus
- /* if (aa.groupRef != null && aa.groupRef.consensusData != null
- && aa.groupRef.isShowSequenceLogo())
- {
- //TODO check what happens for group selections
- return StructureFrequency.extractProfile(
- aa.groupRef.consensusData[column], aa.groupRef
- .getIgnoreGapsConsensus());
- }
- */
+ /*
+ * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
+ * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
+ * group selections return StructureFrequency.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 && hStrucConsensus!=null && hStrucConsensus.length>column)
+ && hStrucConsensus != null
+ && hStrucConsensus.length > column)
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
av_ignoreGapsConsensus);
@@ -186,25 +273,41 @@ public class AnnotationRenderer
}
return null;
}
-
+
/**
- * DOCUMENT ME!
+ * Render the annotation rows associated with an alignment.
*
- * @param annotationPanel TODO
+ * @param annotPanel
+ * container frame
+ * @param av
+ * data and view settings to render
* @param g
- * DOCUMENT ME!
+ * destination for graphics
+ * @param activeRow
+ * row where a mouse event occured (or -1)
* @param startRes
- * DOCUMENT ME!
+ * first column that will be drawn
* @param endRes
- * DOCUMENT ME!
+ * last column that will be drawn
+ * @return true if the fadedImage was used for any alignment annotation rows
+ * currently being calculated
*/
- public void drawComponent(AwtRenderPanelI annotPanel, AlignViewportI av, Graphics g, int activeRow, int startRes, int endRes)
+ public boolean drawComponent(AwtRenderPanelI annotPanel,
+ 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 AlignViewport
+ // AnnotationPanel needs to implement: ImageObserver, access to
+ // AlignViewport
updateFromAwtRenderPanel(annotPanel, av);
+ fm = g.getFontMetrics();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-
+ if (aa==null)
+ {
+ return false;
+ }
int x = 0, y = 0;
int column = 0;
char lastSS;
@@ -216,16 +319,42 @@ public class AnnotationRenderer
boolean centreColLabels, centreColLabelsDef = av
.getCentreColumnLabels();
boolean scaleColLabel = false;
- boolean[] graphGroupDrawn = new boolean[aa.length];
+ AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(),structConsensusAnnot=av.getAlignmentStrucConsensusAnnotation();
+ boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
+
+ 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];
-
+ {
+ // 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)
+ {
+ 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)
{
continue;
@@ -235,16 +364,26 @@ public class AnnotationRenderer
scaleColLabel = row.scaleColLabel;
lastSS = ' ';
lastSSX = 0;
+
+ if (!useClip || ((y-charHeight)=sOffset))
+ {// if_in_visible_region
+ if (!clipst)
+ {
+ clipst=true;
+ yfrom=y;
+ f_i=i;
+ }
+ yto = y;
+ f_to=i;
if (row.graph > 0)
{
- if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
- {
+ if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup)) {
continue;
}
-
+
// this is so that we draw the characters below the graph
y += row.height;
-
+
if (row.hasText)
{
iconOffset = charHeight - fm.getDescent();
@@ -254,50 +393,46 @@ public class AnnotationRenderer
else if (row.hasText)
{
iconOffset = charHeight - fm.getDescent();
-
+
}
else
{
iconOffset = 0;
}
-
- if (aa[i].autoCalculated && av.isCalculationInProgress(aa[i]))
+
+ 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);
-
- 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;
}
- */
+
+ /*
+ * 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;
@@ -305,9 +440,8 @@ public class AnnotationRenderer
{
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(
- startRes + x);
- if (column > row.annotations.length - 1)
+ column = columnSelection.adjustForHiddenColumns(startRes + x);
+ if (column > row_annotations.length - 1)
{
break;
}
@@ -316,9 +450,9 @@ public class AnnotationRenderer
{
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;
}
@@ -331,17 +465,16 @@ public class AnnotationRenderer
if (activeRow == i)
{
g.setColor(Color.red);
-
+
if (columnSelection != null)
{
for (int n = 0; n < columnSelection.size(); n++)
{
int v = columnSelection.columnAt(n);
-
+
if (v == column)
{
- g.fillRect(x * charWidth, y, charWidth,
- charHeight);
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
}
}
}
@@ -349,21 +482,22 @@ public class AnnotationRenderer
if (!row.isValidStruc())
{
g.setColor(Color.orange);
- g.fillRect((int)row.getInvalidStrucPos()*charWidth, y, charWidth, charHeight);
+ g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
+ charWidth, charHeight);
}
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)
{
- fmWidth = (float) fm.charsWidth(
- row.annotations[column].displayCharacter
+ fmWidth = fm.charsWidth(
+ row_annotations[column].displayCharacter
.toCharArray(), 0,
- row.annotations[column].displayCharacter.length());
-
+ row_annotations[column].displayCharacter.length());
+
if (scaleColLabel)
{
// justify the label and scale to fit in column
@@ -381,29 +515,29 @@ public class AnnotationRenderer
}
else
{
- fmWidth = (float) fm
- .charWidth(row.annotations[column].displayCharacter
+ fmWidth = fm
+ .charWidth(row_annotations[column].displayCharacter
.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(row.annotations[column].colour);
-
+ g.setColor(row_annotations[column].colour);
+
if (column == 0 || row.graph > 0)
{
- g.drawString(row.annotations[column].displayCharacter,
+ g.drawString(row_annotations[column].displayCharacter,
(x * charWidth) + charOffset, y + iconOffset);
}
- else if (row.annotations[column - 1] == null
+ 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 == ' ')))
+ || !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);
@@ -411,12 +545,12 @@ public class AnnotationRenderer
}
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 (row.annotations[column].displayCharacter.indexOf(')') > -1)
+ if (row_annotations[column].displayCharacter.indexOf(')') > -1)
{
ss = 's';
}
@@ -428,26 +562,26 @@ public class AnnotationRenderer
switch (lastSS)
{
case 'H':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes, validEnd);
break;
-
+
case 'E':
- drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ 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
- drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ drawStemAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes, validEnd);
break;
-
+
default:
g.setColor(Color.gray);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- lastSSX, 2);
-
+
break;
}
}
@@ -468,17 +602,17 @@ public class AnnotationRenderer
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;
}
- 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;
}
@@ -486,40 +620,41 @@ public class AnnotationRenderer
{
validRes = true;
}
-
+
// x ++;
-
+
if (row.hasIcons)
{
switch (lastSS)
{
case 'H':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
break;
-
+
case 'E':
- drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ 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, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
break;
default:
- drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ 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.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
+ if (row.graphGroup > -1 && !graphGroupDrawn.get(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++)
{
@@ -527,12 +662,11 @@ public class AnnotationRenderer
{
continue;
}
-
+
if (aa[gg] != row)
{
aa[gg].visible = false;
}
-
if (aa[gg].graphMax > groupmax)
{
groupmax = aa[gg].graphMax;
@@ -542,97 +676,129 @@ public class AnnotationRenderer
groupmin = aa[gg].graphMin;
}
}
-
+
for (int gg = 0; gg < aa.length; gg++)
{
if (aa[gg].graphGroup == row.graphGroup)
{
- drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
- groupmax, row.graphHeight);
+ drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
+ endRes, y, groupmin, groupmax, row.graphHeight);
}
}
-
- graphGroupDrawn[row.graphGroup] = true;
+
+ graphGroupDrawn.set(row.graphGroup);
}
else
{
- drawLineGraph( g, row, startRes, endRes, y, row.graphMin,
- row.graphMax, row.graphHeight);
+ drawLineGraph(g, row, row_annotations, 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, row_annotations, startRes, endRes,
+ row.graphMin, row.graphMax, y, renderHistogram,renderProfile,normaliseProfile);
}
}
-
+ } else {
+ if (clipst && !clipend)
+ {
+ clipend = true;
+ }
+ }// end if_in_visible_region
if (row.graph > 0 && row.hasText)
{
y += charHeight;
}
-
+
if (row.graph == 0)
{
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 Color GLYPHLINE_COLOR=Color.gray;
- private Color SHEET_COLOUR=Color.green;
- private Color HELIX_COLOUR=Color.red;
- private Color STEM_COLOUR=Color.blue;
-
-
- public void drawGlyphLine(Graphics g, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
+ private final Color GLYPHLINE_COLOR = Color.gray;
+
+ private final Color SHEET_COLOUR = Color.green;
+
+ private final Color HELIX_COLOUR = Color.red;
+
+ private 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)
{
g.setColor(GLYPHLINE_COLOR);
- 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, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
+ 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);
-
- 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.fillPolygon(
+ 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[]
- { (x * charWidth) - 4, (x * charWidth) - 4,
- (x * charWidth) }, new int[]
{ y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
3);
}
else
{
- g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth
- - lastSSX, 7);
+ g.fillRect(lastSSX, y + 4 + iconOffset,
+ (x + 1) * charWidth - lastSSX, 7);
}
-
+
}
- public void drawHelixAnnot(Graphics g, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
+ public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
+ int x, int y, int iconOffset, int startRes, int column,
+ boolean validRes, boolean validEnd)
{
g.setColor(HELIX_COLOUR);
-
+
int sCol = (lastSSX / charWidth) + startRes;
int x1 = lastSSX;
int x2 = (x * charWidth);
-
+
if (MAC)
{
int ofs = charWidth / 2;
// 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
@@ -641,79 +807,81 @@ public class AnnotationRenderer
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')
{
-
+
}
else
{
// g.setColor(Color.magenta);
g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
+ 1, 8, 0, 0);
-
+
}
-
+
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;
}
-
- 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);
x2 -= charWidth / 2;
}
-
+
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
}
- 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,
+ Annotation[] aa_annotations, int sRes, int eRes, int y,
+ float min, float max, int graphHeight)
{
- if (sRes > aa.annotations.length)
+ if (sRes > aa_annotations.length)
{
return;
}
-
+
int x = 0;
-
+
// Adjustment for fastpaint to left
if (eRes < endRes)
{
eRes++;
}
-
- eRes = Math.min(eRes, aa.annotations.length);
-
+
+ eRes = Math.min(eRes, aa_annotations.length);
+
if (sRes == 0)
{
x++;
}
-
+
int y1 = y, y2 = y;
float range = max - min;
-
+
// //Draw origin
if (min < 0)
{
y2 = y - (int) ((0 - min / range) * graphHeight);
}
-
+
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 aaMax = aa.annotations.length - 1;
-
+ int aaMax = aa_annotations.length - 1;
+
while (x < eRes - sRes)
{
column = sRes + x;
@@ -721,89 +889,74 @@ public class AnnotationRenderer
{
column = columnSelection.adjustForHiddenColumns(column);
}
-
+
if (column > aaMax)
{
break;
}
-
- if (aa.annotations[column] == null
- || aa.annotations[column - 1] == null)
+
+ if (aa_annotations[column] == null
+ || aa_annotations[column - 1] == null)
{
x++;
continue;
}
-
- if (aa.annotations[column].colour == null)
+
+ if (aa_annotations[column].colour == null)
g.setColor(Color.black);
else
- g.setColor(aa.annotations[column].colour);
-
+ g.setColor(aa_annotations[column].colour);
+
y1 = y
- - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
+ - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
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++;
}
-
- 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));
-
- 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());
}
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, float min, float max, int y)
+ public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
+ Annotation[] aa_annotations, int sRes, int eRes, float min,
+ float max, int y, boolean renderHistogram,boolean renderProfile,boolean normaliseProfile)
{
- if (sRes > aa.annotations.length)
+ if (sRes > aa_annotations.length)
{
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;
-
+
float range = max - min;
-
+
if (min < 0)
{
- y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
+ y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
}
-
+
g.setColor(Color.gray);
-
+
g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
-
+
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;
- }
- }
+ int aaMax = aa_annotations.length - 1;
while (x < eRes - sRes)
{
column = sRes + x;
@@ -811,25 +964,25 @@ public class AnnotationRenderer
{
column = columnSelection.adjustForHiddenColumns(column);
}
-
+
if (column > aaMax)
{
break;
}
-
- if (aa.annotations[column] == null)
+
+ if (aa_annotations[column] == null)
{
x++;
continue;
}
- if (aa.annotations[column].colour == null)
+ if (aa_annotations[column].colour == null)
g.setColor(Color.black);
else
- g.setColor(aa.annotations[column].colour);
-
+ g.setColor(aa_annotations[column].colour);
+
y1 = y
- - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
-
+ - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
+
if (renderHistogram)
{
if (y1 - y2 > 0)
@@ -842,27 +995,26 @@ public class AnnotationRenderer
}
}
// draw profile if available
- if (renderProfile && aa.annotations[column].value != 0)
+ 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)
+ 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;
char[] dc;
-
+
/**
- * profl.length == 52 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
+ * 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
*/
- if (profl.length == 52)
+ if (profl.length == 74)
{
dc = new char[2];
}
@@ -870,52 +1022,42 @@ public class AnnotationRenderer
{
dc = new char[1];
}
- LineMetrics lm=g.getFontMetrics(ofont).getLineMetrics("Q", g);
- double scale = 1f/(normaliseProfile ? profl[1] : 100f);
- float ofontHeight = 1f/lm.getAscent();// magnify to fill box
- double scl=0.0;
- for (int c = 2; profl != null && c < profl[0];)
+ LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
+ double scale = 1f / (normaliseProfile ? profl[1] : 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"))
+
+ if (_aa.label.startsWith("StrucConsensus"))
{
dc[1] = (char) profl[c++];
}
-
+
wdth = charWidth;
- wdth /= (float) fm.charsWidth(dc, 0, dc.length);
-
- ht += scl;
+ wdth /= fm.charsWidth(dc, 0, dc.length);
+
+ ht += scl;
{
- // if (aa.annotations[column].value==0) {
- // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
- // (ht2=(aa.graphHeight*0.1/av.charHeight)))));
- // ht = y2-(int)ht2;
- // } else {
- scl=((double)htn)*scale* ((double) profl[c++]);
- lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics().getFontRenderContext());
+ scl = htn * scale * profl[c++];
+ lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
+ .getFontRenderContext());
g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
- wdth, scl/lm.getAscent())));
+ wdth, scl / lm.getAscent())));
lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
-
- // htn -=ht2;
- // }
- // ? );// try to get a
- // colourscheme for the
- // group(aa.groupRef.cs==null)
- // ? av.textColour2 :
- // cs.findColour(dc));
- // System.out.println(dc[0]);
+
// Debug - render boxes around characters
// g.setColor(Color.red);
- // g.drawRect(x*av.charWidth, (int)ht, av.charWidth, (int)(scl));
+ // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
+ // (int)(scl));
// g.setColor(profcolour.findColour(dc[0]).darker());
- g.setColor(profcolour.findColour(dc[0]));
- // (av.globalColourScheme!=null)
- g.drawChars(dc, 0, dc.length, x * charWidth,
- (int) (ht + (scl-lm.getDescent()-lm.getBaselineOffsets()[lm.getBaselineIndex()])));
- // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
+ 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);
}
}
g.setFont(ofont);
@@ -923,24 +1065,26 @@ public class AnnotationRenderer
}
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));
-
- 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
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
- int y, int sRes, int eRes)
+ public void drawGraph(Graphics g, AlignmentAnnotation _aa,
+ Annotation[] aa_annotations, int width, 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));
@@ -949,14 +1093,14 @@ public class AnnotationRenderer
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(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;