+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 jalview.analysis.CodingUtils;
+import jalview.analysis.Rna;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.ProfilesI;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.Platform;
import java.awt.BasicStroke;
import java.awt.Color;
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;
+
+ private int charWidth, endRes, charHeight;
+
+ private boolean validCharWidth, hasHiddenColumns;
+
+ private FontMetrics fm;
+
+ private final boolean MAC = Platform.isAMac();
+
+ boolean av_renderHistogram = true, av_renderProfile = true,
+ av_normaliseProfile = false;
+
+ ResidueShaderI profcolour = null;
+
+ private ColumnSelection columnSelection;
+
+ private HiddenColumns hiddenColumns;
+
+ private ProfilesI hconsensus;
+
+ private Hashtable[] complementConsensus;
+
+ 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 AnnotationRenderer()
{
- // TODO Auto-generated constructor stub
+ this(false);
}
- public void drawStemAnnot(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
+ /**
+ * 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;
+ }
+
+ /**
+ * Remove any references and resources when this object is no longer required
+ */
+ public void dispose()
+ {
+ hiddenColumns = null;
+ hconsensus = null;
+ complementConsensus = null;
+ hStrucConsensus = null;
+ fadedImage = null;
+ annotationPanel = null;
+ }
+
+ 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 sCol = (lastSSX / charWidth)
+ + hiddenColumns.visibleToAbsoluteColumn(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;
+ 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);
+ boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
+ || dc != row_annotations[sCol - 1].secondaryStructure;
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))
+ || row_annotations[column] == null
+ || dc != row_annotations[column].secondaryStructure;
+
+ if (column > 0 && Rna.isClosingParenthesis(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[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ /*
+ * if new annotation with a closing base pair half of the stem,
+ * display a backward arrow
+ */
+ g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+ new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+ 3);
x1 += 5;
}
if (diffdownstream)
// 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);
+ /*
+ * if annotation ending with an opeing base pair half of the stem,
+ * display a forward arrow
+ */
+ g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
+ new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+ 3);
x2 -= 5;
}
if (diffupstream)
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
}
- 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 ColumnSelection columnSelection;
-
- private Hashtable[] hconsensus;
+ 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);
- private Hashtable[] hStrucConsensus;
+ g.setColor(nonCanColor);
+ int sCol = (lastSSX / charWidth)
+ + hiddenColumns.visibleToAbsoluteColumn(startRes);
+ int x1 = lastSSX;
+ int x2 = (x * charWidth);
- private boolean av_ignoreGapsConsensus;
+ String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
+ : row_annotations[column - 1].displayCharacter;
- /**
- * attributes set from AwtRenderPanelI
- */
- /**
- * old image used when data is currently being calculated and cannot be
- * rendered
- */
- private Image fadedImage;
+ 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 && Rna.isClosingParenthesis(dc))
+ {
- /**
- * panel being rendered into
- */
- private ImageObserver annotationPanel;
+ 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
+ {
- /**
- * width of image to render in panel
- */
- private int imgWidth;
+ // 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)
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();
+ endRes = av.getRanges().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)
+ profcolour = av.getResidueShading();
+ if (profcolour == null || profcolour.getColourScheme() == 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();
+ /*
+ * Use default colour for sequence logo if
+ * the alignment has no colourscheme set
+ * (would like to use user preference but n/a for applet)
+ */
+ ColourSchemeI col = av.getAlignment().isNucleotide()
+ ? new NucleotideColourScheme()
+ : new ZappoColourScheme();
+ profcolour = new ResidueShader(col);
}
columnSelection = av.getColumnSelection();
- hconsensus = av.getSequenceConsensusHash();// hconsensus;
- hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus;
- av_ignoreGapsConsensus = av.getIgnoreGapsConsensus();
+ hiddenColumns = av.getAlignment().getHiddenColumns();
+ hconsensus = av.getSequenceConsensusHash();
+ complementConsensus = av.getComplementConsensusHash();
+ hStrucConsensus = av.getRnaStructureConsensusHash();
+ av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
}
- public int[] getProfileFor(AlignmentAnnotation aa, int column)
+ /**
+ * 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
+ */
+ 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.consensusData.get(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.get(column),
+ av_ignoreGapsConsensus);
+ }
}
}
else
// to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
- && av_renderProfile && hStrucConsensus != null
+ && hStrucConsensus != null
&& hStrucConsensus.length > column)
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
return null;
}
+ boolean rna = false;
+
/**
- * 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
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 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)
{
continue;
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;
- }
-
- if (aa[i].autoCalculated && av.isCalculationInProgress(aa[i]))
- {
- y += charHeight;
-
- 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);
+ yto = y;
+ f_to = i;
+ if (row.graph > 0)
+ {
+ if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
+ {
+ continue;
+ }
- continue;
- }
+ // this is so that we draw the characters below the graph
+ y += row.height;
- /*
- * 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 (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;
}
- if (x > -1)
+
+ /*
+ * 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 (activeRow == i)
+ if (hasHiddenColumns)
+ {
+ column = hiddenColumns.visibleToAbsoluteColumn(startRes + x);
+ if (column > row_annotations.length - 1)
+ {
+ break;
+ }
+ }
+ else
{
- g.setColor(Color.red);
+ column = startRes + x;
+ }
- if (columnSelection != null)
+ if ((row_annotations == null)
+ || (row_annotations.length <= column)
+ || (row_annotations[column] == null))
+ {
+ validRes = false;
+ }
+ else
+ {
+ validRes = true;
+ }
+ final String displayChar = validRes
+ ? row_annotations[column].displayCharacter
+ : null;
+ if (x > -1)
+ {
+ if (activeRow == i)
{
- for (int n = 0; n < columnSelection.size(); n++)
- {
- int v = columnSelection.columnAt(n);
+ g.setColor(Color.red);
- if (v == column)
+ if (columnSelection != null)
+ {
+ if (columnSelection.contains(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)
+ 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 = (float) 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)
{
// 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);
+ }
+
+ 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);
}
- else
+ }
+ if (row.hasIcons)
+ {
+ char ss = validRes ? row_annotations[column].secondaryStructure
+ : '-';
+
+ if (ss == '(')
{
- fmWidth = (float) fm
- .charWidth(row.annotations[column].displayCharacter
- .charAt(0));
- }
- charOffset = (int) ((charWidth - fmWidth) / 2f);
+ // distinguish between forward/backward base-pairing
+ if (displayChar.indexOf(')') > -1)
+ {
- if (row.annotations[column].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(row.annotations[column].colour);
+ ss = ')';
- if (column == 0 || row.graph > 0)
+ }
+ }
+ if (ss == '[')
{
- g.drawString(row.annotations[column].displayCharacter,
- (x * charWidth) + charOffset, y + iconOffset);
+ if ((displayChar.indexOf(']') > -1))
+ {
+ ss = ']';
+
+ }
}
- 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 == ' ')))
+ if (ss == '{')
{
- g.drawString(row.annotations[column].displayCharacter, x
- * charWidth + charOffset, y + iconOffset);
+ // distinguish between forward/backward base-pairing
+ if (displayChar.indexOf('}') > -1)
+ {
+ ss = '}';
+
+ }
}
- g.setFont(ofont);
- }
- }
- if (row.hasIcons)
- {
- char ss = validRes ? row.annotations[column].secondaryStructure
- : ' ';
- if (ss == 'S')
- {
- // distinguish between forward/backward base-pairing
- if (row.annotations[column].displayCharacter.indexOf(')') > -1)
+ if (ss == '<')
{
- ss = 's';
+ // distinguish between forward/backward base-pairing
+ if (displayChar.indexOf('<') > -1)
+ {
+ ss = '>';
+
+ }
}
- }
- if (!validRes || (ss != lastSS))
- {
- if (x > -1)
+ if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
{
- switch (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)
{
- case 'H':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- case 'E':
- drawSheetAnnot(g, row, 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);
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- - lastSSX, 2);
-
- break;
+ ss = (char) ssLowerCase;
}
}
- if (validRes)
+
+ if (!validRes || (ss != lastSS))
{
- lastSS = ss;
+
+ 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;
+ }
+ // no break if isRNA - falls through to drawNotCanonicalAnnot!
+ case 'E':
+ if (!isRNA)
+ {
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes,
+ validEnd);
+ break;
+ }
+ // no break if isRNA - fall through to drawNotCanonicalAnnot!
+
+ 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);
+ }
}
- else
+ }
+ 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 'H':
+ if (!isRNA)
{
- lastSS = ' ';
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
}
- if (x > -1)
+ // no break if isRNA - fall through to drawNotCanonicalAnnot!
+
+ case 'E':
+ if (!isRNA)
{
- lastSSX = (x * charWidth);
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
}
- }
- }
- 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;
- }
+ // no break if isRNA - fall through to drawNotCanonicalAnnot!
- // x ++;
+ case '(':
+ case ')': // Stem case for RNA secondary structure
- if (row.hasIcons)
- {
- switch (lastSS)
- {
- case 'H':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- case 'E':
- drawSheetAnnot(g, row, 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);
- break;
- default:
- drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
+ 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)
+ for (int gg = 0; gg < aa.length; gg++)
{
- groupmax = aa[gg].graphMax;
- }
- if (aa[gg].graphMin < groupmin)
- {
- 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], 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, 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, startRes, endRes, row.graphMin,
- row.graphMax, y);
+ 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 Color GLYPHLINE_COLOR = Color.gray;
+ public static final Color GLYPHLINE_COLOR = Color.gray;
- private Color SHEET_COLOUR = Color.green;
+ public static final Color SHEET_COLOUR = Color.green;
- private Color HELIX_COLOUR = Color.red;
+ public static final Color HELIX_COLOUR = Color.red;
- private Color STEM_COLOUR = Color.blue;
+ public static final 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 Color sdNOTCANONICAL_COLOUR;
+
+ 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, AlignmentAnnotation row,
+ 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(new int[]
- { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
+ 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);
+ 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)
+ 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 sCol = (lastSSX / charWidth)
+ + hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
// 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
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);
+ 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.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)
+ 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;
}
eRes++;
}
- eRes = Math.min(eRes, aa.annotations.length);
+ eRes = Math.min(eRes, aa_annotations.length);
if (sRes == 0)
{
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;
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(column);
+ column = hiddenColumns.visibleToAbsoluteColumn(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);
- y2 = y
- - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
+ 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);
+ 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)
+ 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;
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;
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(column);
+ column = hiddenColumns.visibleToAbsoluteColumn(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);
+ y1 = y - (int) (((aa_annotations[column].value - min) / (range))
+ * _aa.graphHeight);
if (renderHistogram)
{
}
}
// draw profile if available
- if (renderProfile && aa.annotations[column].value != 0)
+ if (renderProfile)
{
- int profl[] = getProfileFor(aa, column);
+ /*
+ * {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)
{
- float ht = normaliseProfile ? y - aa.graphHeight : y1;
- double htn = normaliseProfile ? aa.graphHeight : (y2 - y1);// aa.graphHeight;
+ 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;
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
+ * 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 /= (float) fm.charsWidth(dc, 0, dc.length);
+ 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());
+ Font font = ofont.deriveFont(AffineTransform
+ .getScaleInstance(wdth, scl / lm.getAscent()));
+ g.setFont(font);
+ 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 = ((double) htn) * scale * ((double) 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);
}
}
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));
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;
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