/*
* 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;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
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()
{
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,
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);
boolean diffdownstream = !validRes || !validEnd
|| 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))
{
g.fillPolygon(new int[]
{ lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
{ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
x1 += 5;
}
if (diffdownstream)
{
x2 -= 1;
}
}
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);
x2 -= 5;
}
if (diffupstream)
{
x1 += 1;
}
}
// draw arrow body
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
}
private int charWidth, endRes, charHeight;
private boolean validCharWidth, hasHiddenColumns;
private FontMetrics fm;
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
*/
private Image fadedImage;
/**
* panel being rendered into
*/
private ImageObserver annotationPanel;
/**
* width of image to render in panel
*/
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 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);
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;
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);
// 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 (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);
x1 += 5;
}
if (diffdownstream)
{
x2 -= 1;
}
}
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);
x2 -= 5;
}
if (diffupstream)
{
x1 += 1;
}
}
// draw arrow body
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
}
// 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();
// 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();
endRes = av.getEndRes();
charHeight = av.getCharHeight();
hasHiddenColumns = av.hasHiddenColumns();
validCharWidth = av.isValidCharWidth();
av_renderHistogram = av.isShowConsensusHistogram();
av_renderProfile = av.isShowSequenceLogo();
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();
}
columnSelection = av.getColumnSelection();
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
//
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());
}
// TODO extend annotation row to enable dynamic and static profile data to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null)
{
return AAFrequency.extractProfile(hconsensus[column],
av_ignoreGapsConsensus);
}
}
else
{
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()); }
*/
// TODO extend annotation row to enable dynamic and static profile data
// to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
&& hStrucConsensus != null
&& hStrucConsensus.length > column)
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
av_ignoreGapsConsensus);
}
}
}
return null;
}
/**
* Render the annotation rows associated with an alignment.
*
* @param annotPanel
* container frame
* @param av
* data and view settings to render
* @param g
* destination for graphics
* @param activeRow
* row where a mouse event occured (or -1)
* @param startRes
* first column that will be drawn
* @param endRes
* last column that will be drawn
* @return true if the fadedImage was used for any alignment annotation rows
* currently being calculated
*/
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
updateFromAwtRenderPanel(annotPanel, av);
fm = g.getFontMetrics();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int temp = 0;
if (aa==null)
{
return false;
}
int x = 0, y = 0;
int column = 0;
char lastSS;
int lastSSX;
int iconOffset = 0;
boolean validRes = false;
boolean validEnd = false;
boolean labelAllCols = false;
boolean centreColLabels, centreColLabelsDef = av
.getCentreColumnLabels();
boolean scaleColLabel = false;
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;
}
centreColLabels = row.centreColLabels || centreColLabelsDef;
labelAllCols = row.showAllColLabels;
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.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();
y -= charHeight;
}
}
else if (row.hasText)
{
iconOffset = charHeight - fm.getDescent();
}
else
{
iconOffset = 0;
}
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; }
*/
// 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;
}
}
else
{
column = startRes + x;
}
if ((row_annotations == null) || (row_annotations.length <= column)
|| (row_annotations[column] == null))
{
validRes = false;
}
else
{
validRes = true;
}
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 (v == column)
{
g.fillRect(x * charWidth, y, charWidth, charHeight);
}
}
}
}
if (!row.isValidStruc())
{
g.setColor(Color.orange);
g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
charWidth, charHeight);
}
if (validCharWidth
&& validRes
&& row_annotations[column].displayCharacter != null
&& (row_annotations[column].displayCharacter.length() > 0))
{
if (centreColLabels || scaleColLabel)
{
fmWidth = fm.charsWidth(
row_annotations[column].displayCharacter
.toCharArray(), 0,
row_annotations[column].displayCharacter.length());
if (scaleColLabel)
{
// justify the label and scale to fit in column
if (fmWidth > charWidth)
{
// scale only if the current font isn't already small enough
fmScaling = charWidth;
fmScaling /= fmWidth;
g.setFont(ofont.deriveFont(AffineTransform
.getScaleInstance(fmScaling, 1.0)));
// and update the label's width to reflect the scaling.
fmWidth = charWidth;
}
}
}
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);
}
g.setFont(ofont);
}
}
if (row.hasIcons)
{
char ss = validRes ? row_annotations[column].secondaryStructure
: '-';
if (ss == '(')
{
// distinguish between forward/backward base-pairing
if (row_annotations[column].displayCharacter.indexOf(')') > -1)
{
ss = ')';
}
}
if (ss == '[')
{
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 == '<')
{
// distinguish between forward/backward base-pairing
if (row_annotations[column].displayCharacter.indexOf('<') > -1)
{
ss = '>';
}
}
if (ss >=65)
{
// 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)
{
int nb_annot=x-temp;
//System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
switch (lastSS)
{
case '$':
drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
case 'µ':
drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
case '(': // Stem case for RNA secondary structure
case ')': // and opposite direction
drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
temp=x;
break;
case '{':
case '}':
case '[':
case ']':
case '>':
case '<':
case 'A':
case 'a':
case 'B':
case 'b':
case 'C':
case 'c':
case 'D':
case 'd':
case 'E':
case 'e':
case 'F':
case 'f':
case 'G':
case 'g':
case 'H':
case 'h':
case 'I':
case 'i':
case 'J':
case 'j':
case 'K':
case 'k':
case 'L':
case 'l':
case 'M':
case 'm':
case 'N':
case 'n':
case 'O':
case 'o':
case 'P':
case 'p':
case 'Q':
case 'q':
case 'R':
case 'r':
case 'S':
case 's':
case 'T':
case 't':
case 'U':
case 'u':
case 'V':
case 'v':
case 'W':
case 'w':
case 'X':
case 'x':
case 'Y':
case 'y':
case 'Z':
case 'z':
Color nonCanColor= getNotCanonicalColor(lastSS);
drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
temp=x;
break;
default:
g.setColor(Color.gray);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- lastSSX, 2);
temp=x;
break;
}
}
if (validRes)
{
lastSS = ss;
}
else
{
lastSS = ' ';
}
if (x > -1)
{
lastSSX = (x * charWidth);
}
}
}
column++;
x++;
}
if (column >= row_annotations.length)
{
column = row_annotations.length - 1;
validEnd = false;
}
else
{
validEnd = true;
}
if ((row_annotations == null) || (row_annotations.length <= column)
|| (row_annotations[column] == null))
{
validRes = false;
}
else
{
validRes = true;
}
// x ++;
if (row.hasIcons)
{
switch (lastSS)
{
case '$':
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);
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.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++)
{
if (aa[gg].graphGroup != row.graphGroup)
{
continue;
}
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;
}
}
for (int gg = 0; gg < aa.length; gg++)
{
if (aa[gg].graphGroup == row.graphGroup)
{
drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin,
groupmax, row.graphHeight);
}
}
graphGroupDrawn.set(row.graphGroup);
}
else
{
drawLineGraph(g, row, row_annotations, startRes, endRes, y, row.graphMin,
row.graphMax, row.graphHeight);
}
}
else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
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 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;
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);
}
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 == null || row[column] == null
|| row[column].secondaryStructure != 'E')
{
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);
}
else
{
g.fillRect(lastSSX, y + 4 + iconOffset,
(x + 1) * charWidth - lastSSX, 7);
}
}
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[sCol - 1] == null
|| row[sCol - 1].secondaryStructure != 'H')
{
}
else
{
// g.setColor(Color.orange);
g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
0, 0);
}
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[sCol - 1] == null
|| row[sCol - 1].secondaryStructure != 'H')
{
g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
x1 += charWidth / 2;
}
if (!validRes || row[column] == null
|| row[column].secondaryStructure != 'H')
{
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,
Annotation[] aa_annotations, int sRes, int eRes, int y,
float min, float max, int graphHeight)
{
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);
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);
int column;
int aaMax = aa_annotations.length - 1;
while (x < eRes - sRes)
{
column = sRes + x;
if (hasHiddenColumns)
{
column = columnSelection.adjustForHiddenColumns(column);
}
if (column > aaMax)
{
break;
}
if (aa_annotations[column] == null
|| aa_annotations[column - 1] == null)
{
x++;
continue;
}
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);
y2 = y
- (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)
{
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);
g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
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)
{
return;
}
Font ofont = g.getFont();
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);
}
g.setColor(Color.gray);
g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
int column;
int aaMax = aa_annotations.length - 1;
while (x < eRes - sRes)
{
column = sRes + x;
if (hasHiddenColumns)
{
column = columnSelection.adjustForHiddenColumns(column);
}
if (column > aaMax)
{
break;
}
if (aa_annotations[column] == null)
{
x++;
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);
if (renderHistogram)
{
if (y1 - y2 > 0)
{
g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
}
else
{
g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
}
}
// draw profile if available
if (renderProfile)
{
int profl[] = getProfileFor(_aa, column);
// 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;
double hght;
float wdth;
double ht2 = 0;
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
*/
if (profl.length == 74)
{
dc = new char[2];
}
else
{
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; c < profl[0];)
{
dc[0] = (char) profl[c++];
if (_aa.label.startsWith("StrucConsensus"))
{
dc[1] = (char) profl[c++];
}
wdth = charWidth;
wdth /= fm.charsWidth(dc, 0, dc.length);
ht += scl;
{
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);
}
}
g.setFont(ofont);
}
}
x++;
}
if (_aa.threshold != null)
{
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);
g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
// used by overview window
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);
g.setColor(Color.white);
g.fillRect(0, 0, width, y);
g.setColor(new Color(0, 0, 180));
int x = 0, height;
for (int j = sRes; j < eRes; j++)
{
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)
{
height = y;
}
g.fillRect(x, y - height, charWidth, height);
}
x += charWidth;
}
}
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;
}
}
}