+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.renderer;
import jalview.analysis.AAFrequency;
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, 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;
* 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, Annotation[] row_annotations,
+ 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(NOTCANONICAL_COLOUR);
+ g.setColor(nonCanColor);
int sCol = (lastSSX / charWidth) + startRes;
int x1 = lastSSX;
int x2 = (x * charWidth);
- Regex closeparen = new Regex("(}|]|a|b|c|d)");
+ Regex closeparen = new Regex("}|]|<|[a-z]");
String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
: row_annotations[column - 1].displayCharacter;
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);
}
}
// 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);
// to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
- && av_renderProfile && hStrucConsensus != null
+ && hStrucConsensus != null
&& hStrucConsensus.length > column)
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
/**
* Render the annotation rows associated with an alignment.
+ *
* @param annotPanel
* container frame
* @param av
* 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
+ * @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)
+ public boolean drawComponent(AwtRenderPanelI annotPanel,
+ AlignViewportI av, Graphics g, int activeRow, int startRes,
+ int endRes)
{
- boolean usedFaded=false;
+ 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;
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];
- Annotation[] row_annotations=row.annotations;
+ {
+ // 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;
scaleColLabel = row.scaleColLabel;
lastSS = ' ';
lastSSX = 0;
+
+ if (!useClip || ((y-charHeight)<visHeight && (y+row.height+charHeight*2)>=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;
}
if (row.autoCalculated && av.isCalculationInProgress(row))
{
y += charHeight;
- usedFaded=true;
+ usedFaded = true;
g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
- row.height, imgWidth, y, annotationPanel);
g.setColor(Color.black);
/*
* 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
.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);
if (row.hasIcons)
{
char ss = validRes ? row_annotations[column].secondaryStructure
- : ' ';
- //System.out.println(ss);
- if (ss == 'S')
+ : '-';
+
+ if (ss == '(')
{
// distinguish between forward/backward base-pairing
if (row_annotations[column].displayCharacter.indexOf(')') > -1)
{
- ss = 's';
- System.out.println(ss);
+
+ ss = ')';
+
}
}
- if (ss == 'C')
+ if (ss == '[')
{
- if ((row_annotations[column].displayCharacter.indexOf(']') > -1) || (row_annotations[column].displayCharacter.indexOf('}') > -1))
+ if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
{
- ss = 'c';
- System.out.println(ss);
+ 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 'H':
+ {
+
+ case '$':
drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
- case 'E':
+ case 'µ':
drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
- case 'S': // Stem case for RNA secondary structure
- case 's': // and opposite direction
+ case '(': // Stem case for RNA secondary structure
+ case ')': // and opposite direction
drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
+ temp=x;
break;
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
case 'C':
case 'c':
- drawNotCanonicalAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ case 'D':
+ case 'd':
+ case 'E':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case 'H':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'S':
+ case 's':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+
+ Color nonCanColor= getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
+ temp=x;
break;
default:
g.setColor(Color.gray);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- lastSSX, 2);
-
+ temp=x;
break;
}
}
{
switch (lastSS)
{
- case 'H':
+ case '$':
drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
- case 'E':
+ 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 'C':
- drawNotCanonicalAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ 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:
{
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++)
{
{
aa[gg].visible = false;
}
-
if (aa[gg].graphMax > groupmax)
{
groupmax = aa[gg].graphMax;
}
}
- graphGroupDrawn[row.graphGroup] = true;
+ graphGroupDrawn.set(row.graphGroup);
}
else
{
}
else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
- drawBarGraph(g, row, row_annotations, 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;
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 STEM_COLOUR = Color.blue;
- private final Color NOTCANONICAL_COLOUR = Color.red;
+ private Color sdNOTCANONICAL_COLOUR;
public void drawGlyphLine(Graphics g, Annotation[] row,
int lastSSX, int x, int y, int iconOffset, int startRes,
{
g.setColor(SHEET_COLOUR);
- if (!validEnd || !validRes || row==null || row[column] == null
+ if (!validEnd || !validRes || row == null || row[column] == null
|| row[column].secondaryStructure != 'E')
{
g.fillRect(lastSSX, y + 4 + iconOffset,
}
- public void drawHelixAnnot(Graphics g, Annotation[] 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);
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)
+ 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)
{
}
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, 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)
{
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;
// 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));
+ g.setColor(profcolour.findColour(dc[0], column, null));
hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
.getBaselineIndex()]));
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, Annotation[] aa_annotations, 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);
g.setColor(Color.white);
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;
+
+ }
+ }
}
+
+
+
git://source.jalview.org / jalview.git / blobdiff