import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
showFeatures = true;
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+
PDBChain chain;
if (bysequence && pdb != null)
{
tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
if (showFeatures)
{
- tmp.startCol = fr.findFeatureColour(tmp.startCol,
+ tmp.startCol = finder.findFeatureColour(tmp.startCol,
sequence[s], pos);
}
}
tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);
if (showFeatures)
{
- tmp.endCol = fr.findFeatureColour(tmp.endCol,
+ tmp.endCol = finder.findFeatureColour(tmp.endCol,
sequence[s], pos);
}
}
-
}
}
}
import jalview.gui.SequenceRenderer;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
showFeatures = true;
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
PDBChain chain;
if (bysequence && pdb != null)
{
tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
if (showFeatures)
{
- tmp.startCol = fr.findFeatureColour(tmp.startCol,
+ tmp.startCol = finder.findFeatureColour(tmp.startCol,
sequence[s], pos);
}
}
tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);
if (showFeatures)
{
- tmp.endCol = fr.findFeatureColour(tmp.endCol,
+ tmp.endCol = finder.findFeatureColour(tmp.endCol,
sequence[s], pos);
}
}
import jalview.datamodel.SequenceI;
import java.awt.Color;
+import java.awt.Graphics;
import java.util.List;
import java.util.Map;
* - sequence providing features
* @param r
* - column position
+ * @param g
* @return
*/
- Color findFeatureColour(Color col, SequenceI sequenceI, int r);
+ Color findFeatureColour(Color col, SequenceI sequenceI, int r, Graphics g);
/**
* trigger the feature discovery process for a newly created feature renderer.
*/
void setVisible(String featureType);
+ /**
+ * Sets the transparency value, between 0 (full transparency) and 1 (no
+ * transparency)
+ *
+ * @param value
+ */
+ void setTransparency(float value);
+
+ /**
+ * Returns the transparency value, between 0 (full transparency) and 1 (no
+ * transparency)
+ *
+ * @return
+ */
+ float getTransparency();
}
package jalview.api;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import java.awt.Color;
Color getResidueBoxColour(SequenceI sequenceI, int r);
- Color getResidueColour(SequenceI seq, int position, FeatureRenderer fr);
+ Color getResidueColour(SequenceI seq, int position,
+ FeatureColourFinder finder);
}
public jalview.api.FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (AlignmentPanel) alignment;
- if (appletJmolBinding.ap.av.isShowSequenceFeatures())
+ AlignmentPanel alignPanel = (AlignmentPanel) alignment;
+ if (alignPanel.av.isShowSequenceFeatures())
{
- if (appletJmolBinding.fr == null)
- {
- appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(
- appletJmolBinding.ap.av);
- }
-
- appletJmolBinding.fr
- .transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
+ return alignPanel.getFeatureRenderer();
+ }
+ else
+ {
+ return null;
}
-
- return appletJmolBinding.fr;
}
@Override
@Override
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (AlignmentPanel) alignment;
- if (ap.av.isShowSequenceFeatures())
+ AlignmentPanel alignPanel = (AlignmentPanel) alignment;
+ if (alignPanel.av.isShowSequenceFeatures())
{
- return ap.getFeatureRenderer();
+ return alignPanel.getFeatureRenderer();
}
else
{
package jalview.appletgui;
import jalview.datamodel.AlignmentI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import java.awt.Color;
import java.awt.Dimension;
.hasHiddenColumns();
boolean hiddenRow = false;
AlignmentI alignment = av.getAlignment();
+
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
for (row = 0; row <= sequencesHeight; row++)
{
if (resizeAgain)
if (av.isShowSequenceFeatures())
{
- color = fr.findFeatureColour(color, seq, lastcol);
+ color = finder.findFeatureColour(color, seq, lastcol);
}
}
else
if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * avcharHeight));
+ + ((i - startSeq) * avcharHeight), false);
}
// / Highlight search Results once all sequences have been drawn
*/
package jalview.appletgui;
-import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import java.awt.Color;
import java.awt.Font;
*
* @param seq
* @param position
- * @param fr
+ * @param finder
* @return
*/
@Override
public Color getResidueColour(final SequenceI seq, int position,
- FeatureRenderer fr)
+ FeatureColourFinder finder)
{
// TODO replace 8 or so code duplications with calls to this method
// (refactored as needed)
Color col = getResidueBoxColour(seq, position);
- if (fr != null)
+ if (finder != null)
{
- col = fr.findFeatureColour(col, seq, position);
+ col = finder.findFeatureColour(col, seq, position);
}
return col;
}
*/
package jalview.ext.jmol;
-import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
/**
* @param files
* @param sr
- * @param fr
- * @param viewport
+ * @param viewPanel
* @return
*/
@Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
{
return JmolCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, fr, viewport);
+ getSequence(), sr, viewPanel);
}
/**
if (notifyLoaded)
{
FeatureRenderer fr = getFeatureRenderer(null);
- if (fr != null)
- {
- fr.featuresAdded();
- }
+ fr.featuresAdded();
refreshGUI();
loadNotifiesHandled++;
}
package jalview.ext.jmol;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
*/
public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
{
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+ AlignViewportI viewport = viewPanel.getAlignViewport();
ColumnSelection cs = viewport.getColumnSelection();
AlignmentI al = viewport.getAlignment();
List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
if (fr != null)
{
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+ col = finder
+ .findFeatureColour(col, sequence[pdbfnum][s], r);
}
/*
package jalview.ext.rbvi.chimera;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
* @param sequence
* @param sr
* @param fr
- * @param viewport
+ * @param viewPanel
* @return
*/
public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
{
Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
- sequence, sr, fr, viewport);
+ sequence, sr, viewPanel);
List<String> colourCommands = buildColourCommands(colourMap);
*/
protected static Map<Object, AtomSpecModel> buildColoursMap(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
{
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+ AlignViewportI viewport = viewPanel.getAlignViewport();
ColumnSelection cs = viewport.getColumnSelection();
AlignmentI al = viewport.getAlignment();
Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
continue;
}
- Color colour = sr.getResidueColour(seq, r, fr);
+ Color colour = sr.getResidueColour(seq, r, finder);
/*
* darker colour for hidden regions
* @param ssm
* @param files
* @param seqs
- * @param fr
- * @param alignment
+ * @param viewPanel
* @return
*/
public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+ SequenceI[][] seqs, AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
- ssm, files, seqs, fr, alignment);
+ ssm, files, seqs, viewPanel);
List<String> commands = buildSetAttributeCommands(featureMap);
* @param ssm
* @param files
* @param seqs
- * @param fr
- * @param alignment
+ * @param viewPanel
* @return
*/
protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+ SequenceI[][] seqs, AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ if (fr == null)
+ {
+ return theMap;
+ }
+
List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
if (visibleFeatures.isEmpty())
{
return theMap;
}
+ AlignmentI alignment = viewPanel.getAlignment();
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
*/
package jalview.ext.rbvi.chimera;
-import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
{
getSsm().addStructureViewerListener(this);
// ssm.addSelectionListener(this);
- FeatureRenderer fr = getFeatureRenderer(null);
- if (fr != null)
- {
- fr.featuresAdded();
- }
refreshGUI();
}
return true;
/**
* @param files
* @param sr
- * @param fr
- * @param viewport
+ * @param viewPanel
* @return
*/
@Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
{
return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, fr, viewport);
+ getSequence(), sr, viewPanel);
}
/**
{
// TODO refactor as required to pull up to an interface
AlignmentI alignment = avp.getAlignment();
- FeatureRenderer fr = getFeatureRenderer(avp);
-
- /*
- * fr is null if feature display is turned off
- */
- if (fr == null)
- {
- return 0;
- }
String[] files = getPdbFile();
if (files == null)
StructureMappingcommandSet commandSet = ChimeraCommands
.getSetAttributeCommandsForFeatures(getSsm(), files,
- getSequence(), fr, alignment);
+ getSequence(), avp);
String[] commands = commandSet.commands;
if (commands.length > 10)
{
*/
package jalview.ext.varna;
-import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
*/
public static String[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
+ SequenceI[][] sequence, SequenceRenderer sr,
+ FeatureColourFinder fr,
AlignmentI alignment)
{
ArrayList<String> str = new ArrayList<String>();
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
if (mapping == null || mapping.length < 1)
+ {
continue;
+ }
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos < 1 || pos == lastPos)
+ {
continue;
+ }
lastPos = pos;
Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
if (fr != null)
+ {
col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+ }
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
+ "/"
{
private AppJmol appJmolWindow;
- private FeatureRenderer fr = null;
-
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
{
}
@Override
- public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
- {
- AlignmentPanel ap = (alignment == null) ? appJmolWindow
- .getAlignmentPanel() : (AlignmentPanel) alignment;
- if (ap.av.isShowSequenceFeatures())
- {
- if (fr == null)
- {
- fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
- }
- else
- {
- ap.updateFeatureRenderer(fr);
- }
- }
-
- return fr;
- }
-
- @Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
{
return appJmolWindow;
}
+
+ @Override
+ public jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
+ {
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow
+ .getAlignmentPanel() : (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
+ {
+ return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
+ }
+
+ return null;
+ }
}
import javax.swing.JColorChooser;
import javax.swing.JComboBox;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JSpinner;
* @version $Revision$
*/
public class FeatureRenderer extends
- jalview.renderer.seqfeatures.FeatureRenderer implements
- jalview.api.FeatureRenderer
+ jalview.renderer.seqfeatures.FeatureRenderer
{
Color resBoxColour;
{
private ChimeraViewFrame cvf;
- private FeatureRenderer fr = null;
-
-
public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
SequenceI[][] sequenceIs, DataSourceType protocol)
: (AlignmentPanel) alignment;
if (ap.av.isShowSequenceFeatures())
{
- if (fr == null)
- {
- fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
- }
- else
- {
- ap.updateFeatureRenderer(fr);
- }
+ return ap.getSeqPanel().seqCanvas.fr;
}
- return fr;
+ return null;
}
@Override
package jalview.gui;
import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import java.awt.Color;
import java.awt.Dimension;
float sampleRow = (float) alheight / (float) sequencesHeight;
int lastcol = -1, lastrow = -1;
- int color = Color.white.getRGB();
+ Color color = Color.white;
int row, col;
jalview.datamodel.SequenceI seq;
final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
// get hidden row and hidden column map once at beginning.
// clone featureRenderer settings to avoid race conditions... if state is
// updated just need to refresh again
+
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+
for (row = 0; row < sequencesHeight; row++)
{
if (resizeAgain)
if ((int) (col * sampleCol) == lastcol
&& (int) (row * sampleRow) == lastrow)
{
- miniMe.setRGB(col, row, color);
+ miniMe.setRGB(col, row, color.getRGB());
continue;
}
if (seq.getLength() > lastcol)
{
- color = sr.getResidueBoxColour(seq, lastcol).getRGB();
+ color = sr.getResidueBoxColour(seq, lastcol);
if (av.isShowSequenceFeatures())
{
- color = fr.findFeatureColour(color, seq, lastcol);
+ color = finder.findFeatureColour(color, seq, lastcol);
}
}
else
{
- color = -1; // White
+ color = Color.WHITE;
}
if (hiddenRow
|| (hasHiddenCols && !av.getColumnSelection().isVisible(
lastcol)))
{
- color = new Color(color).darker().darker().getRGB();
+ color = color.darker().darker();
}
- miniMe.setRGB(col, row, color);
+ miniMe.setRGB(col, row, color.getRGB());
}
}
if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * charHeight));
+ + ((i - startSeq) * charHeight), false);
}
// / Highlight search Results once all sequences have been drawn
*/
package jalview.gui;
-import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.util.Comparison;
import java.awt.Color;
*
* @param seq
* @param position
- * @param fr
+ * @param finder
* @return
*/
@Override
public Color getResidueColour(final SequenceI seq, int position,
- FeatureRenderer fr)
+ FeatureColourFinder finder)
{
// TODO replace 8 or so code duplications with calls to this method
// (refactored as needed)
Color col = getResidueBoxColour(seq, position);
- if (fr != null)
+ if (finder != null)
{
- col = fr.findFeatureColour(col, seq, position);
+ col = finder.findFeatureColour(col, seq, position);
}
return col;
}
import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
import jalview.json.binding.biojson.v1.SequenceGrpPojo;
import jalview.json.binding.biojson.v1.SequencePojo;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.schemes.JalviewColourScheme;
import jalview.schemes.ResidueColourScheme;
import jalview.util.ColorUtils;
return sequenceFeaturesPojo;
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+
for (SequenceI seq : sqs)
{
SequenceI dataSetSequence = seq.getDatasetSequence();
String.valueOf(seq.hashCode()));
String featureColour = (fr == null) ? null : jalview.util.Format
- .getHexString(fr.findFeatureColour(Color.white, seq,
+ .getHexString(finder.findFeatureColour(Color.white, seq,
seq.findIndex(sf.getBegin())));
jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
jsonFeature.setXend(seq.findIndex(sf.getEnd()));
ArrayList<String[]> ccomands = new ArrayList<String[]>();
ArrayList<String> pdbfn = new ArrayList<String>();
StructureMappingcommandSet[] colcommands = JmolCommands
- .getColourBySequenceCommand(ssm, modelSet, sequence, sr, fr,
- ((AlignmentViewPanel) source).getAlignViewport());
+ .getColourBySequenceCommand(ssm, modelSet, sequence, sr,
+ (AlignmentViewPanel) source);
if (colcommands == null)
{
return;
--- /dev/null
+package jalview.renderer.seqfeatures;
+
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.image.BufferedImage;
+
+/**
+ * A helper class to find feature colour using an associated FeatureRenderer
+ *
+ * @author gmcarstairs
+ *
+ */
+public class FeatureColourFinder
+{
+ /*
+ * the class we delegate feature finding to
+ */
+ private jalview.api.FeatureRenderer featureRenderer;
+
+ /*
+ * a 1-pixel image on which features can be drawn, for the case where
+ * transparency allows 'see-through' of multiple feature colours
+ */
+ private BufferedImage offscreenImage;
+
+ /**
+ * Constructor
+ *
+ * @param fr
+ */
+ public FeatureColourFinder(jalview.api.FeatureRenderer fr)
+ {
+ featureRenderer = fr;
+ offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
+ }
+
+ /**
+ * Answers the feature colour to show for the given sequence and column
+ * position. This delegates to the FeatureRenderer to find the colour, which
+ * will depend on feature location, visibility, ordering, and whether or not
+ * transparency is applied. For feature rendering with transparency, this
+ * class provides a dummy 'offscreen' graphics context where multiple feature
+ * colours can be overlaid and the combined colour read back.
+ *
+ * @param defaultColour
+ * @param seq
+ * @param column
+ * @return
+ */
+ public Color findFeatureColour(Color defaultColour, SequenceI seq,
+ int column)
+ {
+ if (!((FeatureRendererModel) featureRenderer).hasRenderOrder())
+ {
+ return defaultColour;
+ }
+
+ FeaturesDisplayedI displayed = featureRenderer.getFeaturesDisplayed();
+ if (displayed == null || displayed.getVisibleFeatureCount() == 0)
+ {
+ return defaultColour; // nothing to see here folks
+ }
+
+ Graphics g = featureRenderer.getTransparency() == 1f ? null
+ : offscreenImage.getGraphics();
+
+ Color c = featureRenderer.findFeatureColour(defaultColour, seq, column,
+ g);
+ if (c != null && g != null)
+ {
+ c = new Color(offscreenImage.getRGB(0, 0));
+ }
+ return c == null ? defaultColour : c;
+ }
+}
import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import java.awt.AlphaComposite;
public class FeatureRenderer extends FeatureRendererModel
{
-
- FontMetrics fm;
-
- int charOffset;
-
- boolean offscreenRender = false;
+ private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
+ .getInstance(AlphaComposite.SRC_OVER, 1.0f);
protected SequenceI lastSeq;
- char s;
-
- int i;
-
- int av_charHeight, av_charWidth;
+ BufferedImage offscreenImage;
- boolean av_validCharWidth, av_isShowSeqFeatureHeight;
+ private volatile SequenceFeature[] lastSequenceFeatures;
- private Integer currentColour;
+ int sfSize;
/**
* Constructor given a viewport
this.av = viewport;
}
- protected void updateAvConfig()
+ /**
+ * Renders the sequence using the given feature colour between the given start
+ * and end columns. Returns true if at least one column is drawn, else false
+ * (the feature range does not overlap the start and end positions).
+ *
+ * @param g
+ * @param seq
+ * @param featureStart
+ * @param featureEnd
+ * @param featureColour
+ * @param start
+ * @param end
+ * @param y1
+ * @param colourOnly
+ * @return
+ */
+ boolean renderFeature(Graphics g, SequenceI seq, int featureStart,
+ int featureEnd, Color featureColour, int start, int end, int y1,
+ boolean colourOnly)
{
- av_charHeight = av.getCharHeight();
- av_charWidth = av.getCharWidth();
- av_validCharWidth = av.isValidCharWidth();
- av_isShowSeqFeatureHeight = av.isShowSequenceFeaturesHeight();
- }
+ int charHeight = av.getCharHeight();
+ int charWidth = av.getCharWidth();
+ boolean validCharWidth = av.isValidCharWidth();
- void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
- Color featureColour, int start, int end, int y1)
- {
- updateAvConfig();
- if (((fstart <= end) && (fend >= start)))
+ if (featureStart > end || featureEnd < start)
{
- if (fstart < start)
- { // fix for if the feature we have starts before the sequence start,
- fstart = start; // but the feature end is still valid!!
- }
-
- if (fend >= end)
- {
- fend = end;
- }
- int pady = (y1 + av_charHeight) - av_charHeight / 5;
- for (i = fstart; i <= fend; i++)
- {
- s = seq.getCharAt(i);
+ return false;
+ }
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
+ if (featureStart < start)
+ {
+ featureStart = start;
+ }
+ if (featureEnd >= end)
+ {
+ featureEnd = end;
+ }
+ int pady = (y1 + charHeight) - charHeight / 5;
- g.setColor(featureColour);
+ FontMetrics fm = g.getFontMetrics();
+ for (int i = featureStart; i <= featureEnd; i++)
+ {
+ char s = seq.getCharAt(i);
- g.fillRect((i - start) * av_charWidth, y1, av_charWidth,
- av_charHeight);
+ if (Comparison.isGap(s))
+ {
+ continue;
+ }
- if (offscreenRender || !av_validCharWidth)
- {
- continue;
- }
+ g.setColor(featureColour);
- g.setColor(Color.white);
- charOffset = (av_charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (av_charWidth * (i - start)), pady);
+ g.fillRect((i - start) * charWidth, y1, charWidth,
+ charHeight);
+ if (colourOnly || !validCharWidth)
+ {
+ continue;
}
+
+ g.setColor(Color.white);
+ int charOffset = (charWidth - fm.charWidth(s)) / 2;
+ g.drawString(String.valueOf(s), charOffset
+ + (charWidth * (i - start)), pady);
}
+ return true;
}
- void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend,
- Color featureColour, int start, int end, int y1, byte[] bs)
+ /**
+ * Renders the sequence using the given SCORE feature colour between the given
+ * start and end columns. Returns true if at least one column is drawn, else
+ * false (the feature range does not overlap the start and end positions).
+ *
+ * @param g
+ * @param seq
+ * @param fstart
+ * @param fend
+ * @param featureColour
+ * @param start
+ * @param end
+ * @param y1
+ * @param bs
+ * @param colourOnly
+ * @return
+ */
+ boolean renderScoreFeature(Graphics g, SequenceI seq, int fstart,
+ int fend, Color featureColour, int start, int end, int y1,
+ byte[] bs, boolean colourOnly)
{
- updateAvConfig();
- if (((fstart <= end) && (fend >= start)))
+ if (fstart > end || fend < start)
{
- if (fstart < start)
- { // fix for if the feature we have starts before the sequence start,
- fstart = start; // but the feature end is still valid!!
- }
+ return false;
+ }
- if (fend >= end)
+ if (fstart < start)
+ { // fix for if the feature we have starts before the sequence start,
+ fstart = start; // but the feature end is still valid!!
+ }
+
+ if (fend >= end)
+ {
+ fend = end;
+ }
+ int charHeight = av.getCharHeight();
+ int pady = (y1 + charHeight) - charHeight / 5;
+ int ystrt = 0, yend = charHeight;
+ if (bs[0] != 0)
+ {
+ // signed - zero is always middle of residue line.
+ if (bs[1] < 128)
{
- fend = end;
- }
- int pady = (y1 + av_charHeight) - av_charHeight / 5;
- int ystrt = 0, yend = av_charHeight;
- if (bs[0] != 0)
- {
- // signed - zero is always middle of residue line.
- if (bs[1] < 128)
- {
- yend = av_charHeight * (128 - bs[1]) / 512;
- ystrt = av_charHeight - yend / 2;
- }
- else
- {
- ystrt = av_charHeight / 2;
- yend = av_charHeight * (bs[1] - 128) / 512;
- }
+ yend = charHeight * (128 - bs[1]) / 512;
+ ystrt = charHeight - yend / 2;
}
else
{
- yend = av_charHeight * bs[1] / 255;
- ystrt = av_charHeight - yend;
-
+ ystrt = charHeight / 2;
+ yend = charHeight * (bs[1] - 128) / 512;
}
- for (i = fstart; i <= fend; i++)
- {
- s = seq.getCharAt(i);
+ }
+ else
+ {
+ yend = charHeight * bs[1] / 255;
+ ystrt = charHeight - yend;
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
+ }
- g.setColor(featureColour);
- int x = (i - start) * av_charWidth;
- g.drawRect(x, y1, av_charWidth, av_charHeight);
- g.fillRect(x, y1 + ystrt, av_charWidth, yend);
+ FontMetrics fm = g.getFontMetrics();
+ int charWidth = av.getCharWidth();
- if (offscreenRender || !av_validCharWidth)
- {
- continue;
- }
+ for (int i = fstart; i <= fend; i++)
+ {
+ char s = seq.getCharAt(i);
- g.setColor(Color.black);
- charOffset = (av_charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (av_charWidth * (i - start)), pady);
+ if (Comparison.isGap(s))
+ {
+ continue;
}
- }
- }
- BufferedImage offscreenImage;
+ g.setColor(featureColour);
+ int x = (i - start) * charWidth;
+ g.drawRect(x, y1, charWidth, charHeight);
+ g.fillRect(x, y1 + ystrt, charWidth, yend);
- @Override
- public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
- {
- return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
+ if (colourOnly || !av.isValidCharWidth())
+ {
+ continue;
+ }
+
+ g.setColor(Color.black);
+ int charOffset = (charWidth - fm.charWidth(s)) / 2;
+ g.drawString(String.valueOf(s), charOffset
+ + (charWidth * (i - start)), pady);
+ }
+ return true;
}
/**
* This is used by Structure Viewers and the Overview Window to get the
- * feature colour of the rendered sequence, returned as an RGB value
+ * feature colour of the rendered sequence
*
* @param defaultColour
* @param seq
* @param column
* @return
*/
- public synchronized int findFeatureColour(int defaultColour,
- final SequenceI seq, int column)
+ @Override
+ public Color findFeatureColour(Color defaultColour, SequenceI seq,
+ int column, Graphics g)
{
if (!av.isShowSequenceFeatures())
{
return defaultColour;
}
- if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
+ if (Comparison.isGap(lastSeq.getCharAt(column)))
{
- return Color.white.getRGB();
+ return Color.white;
}
- // Only bother making an offscreen image if transparency is applied
- if (transparency != 1.0f && offscreenImage == null)
+ Color renderedColour = null;
+ if (transparency == 1.0f)
{
- offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
- }
-
- currentColour = null;
- // TODO: non-threadsafe - each rendering thread needs its own instance of
- // the feature renderer - or this should be synchronized.
- offscreenRender = true;
-
- if (offscreenImage != null)
- {
- offscreenImage.setRGB(0, 0, defaultColour);
- drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
-
- return offscreenImage.getRGB(0, 0);
+ renderedColour = findFeatureColour(seq, seq.findPosition(column));
}
else
{
- drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
-
- if (currentColour == null)
- {
- return defaultColour;
- }
- else
- {
- return currentColour.intValue();
- }
+ renderedColour = drawSequence(g, lastSeq, column, column, 0, true);
}
-
+ return renderedColour == null ? defaultColour : renderedColour;
}
- private volatile SequenceFeature[] lastSequenceFeatures;
-
- int sfSize;
-
- int sfindex;
-
- int spos;
-
- int epos;
-
/**
- * Draws the sequence on the graphics context, or just determines the colour
- * that would be drawn (if flag offscreenrender is true).
+ * Draws the sequence features on the graphics context, or just determines the
+ * colour that would be drawn (if flag offscreenrender is true).
*
* @param g
+ * the graphics context to draw on (may be null if colourOnly==true)
* @param seq
* @param start
* start column (or sequence position in offscreenrender mode)
* end column (not used in offscreenrender mode)
* @param y1
* vertical offset at which to draw on the graphics
+ * @param colourOnly
+ * if true, only do enough to determine the colour for the position,
+ * do not draw the character
+ * @return
*/
- public synchronized void drawSequence(Graphics g, final SequenceI seq,
- int start, int end, int y1)
+ public synchronized Color drawSequence(final Graphics g,
+ final SequenceI seq, int start, int end, int y1,
+ boolean colourOnly)
{
SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
if (sequenceFeatures == null || sequenceFeatures.length == 0)
{
- return;
- }
-
- if (g != null)
- {
- fm = g.getFontMetrics();
+ return null;
}
updateFeatures();
lastSequenceFeatures = sequenceFeatures;
}
- if (transparency != 1 && g != null)
+ if (transparency != 1f && g != null)
{
Graphics2D g2 = (Graphics2D) g;
g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
transparency));
}
- if (!offscreenRender)
- {
- spos = lastSeq.findPosition(start);
- epos = lastSeq.findPosition(end);
- }
+ int startPos = lastSeq.findPosition(start);
+ int endPos = lastSeq.findPosition(end);
sfSize = lastSequenceFeatures.length;
+ Color drawnColour = null;
+
+ /*
+ * iterate over features in ordering of their rendering;
+ * if drawing a range of columns, use render order to ensure last is on top
+ * if drawing a single column (as in findFeatureColour), with no
+ * transparency, work backwards to find the topmost rendered feature colour
+ */
for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
{
String type = renderOrder[renderIndex];
// loop through all features in sequence to find
// current feature to render
- for (sfindex = 0; sfindex < sfSize; sfindex++)
+ for (int sfindex = 0; sfindex < sfSize; sfindex++)
{
final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex];
if (!sequenceFeature.type.equals(type))
* unless doing offscreenRender (to the Overview window or a
* structure viewer) which is not limited
*/
- if (!offscreenRender
- && (sequenceFeature.getBegin() > epos || sequenceFeature
- .getEnd() < spos))
+ if (sequenceFeature.getBegin() > endPos
+ || sequenceFeature.getEnd() < startPos)
{
continue;
}
Color featureColour = getColour(sequenceFeature);
boolean isContactFeature = sequenceFeature.isContactFeature();
- if (offscreenRender && offscreenImage == null)
+ if (isContactFeature)
{
- /*
- * offscreen mode with no image (image is only needed if transparency
- * is applied to feature colours) - just check feature is rendered at
- * the requested position (start == sequence position in this mode)
- */
- boolean featureIsAtPosition = sequenceFeature.begin <= start
- && sequenceFeature.end >= start;
- if (isContactFeature)
- {
- featureIsAtPosition = sequenceFeature.begin == start
- || sequenceFeature.end == start;
- }
- if (featureIsAtPosition)
- {
- // this is passed out to the overview and other sequence renderers
- // (e.g. molecule viewer) to get displayed colour for rendered
- // sequence
- currentColour = new Integer(featureColour.getRGB());
- // used to be retreived from av.featuresDisplayed
- // currentColour = av.featuresDisplayed
- // .get(sequenceFeatures[sfindex].type);
-
- }
- }
- else if (isContactFeature)
- {
- renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
+ boolean drawn = renderFeature(g, seq,
+ seq.findIndex(sequenceFeature.begin) - 1,
seq.findIndex(sequenceFeature.begin) - 1, featureColour,
- start, end, y1);
- renderFeature(g, seq, seq.findIndex(sequenceFeature.end) - 1,
+ start, end, y1, colourOnly);
+ drawn |= renderFeature(g, seq,
+ seq.findIndex(sequenceFeature.end) - 1,
seq.findIndex(sequenceFeature.end) - 1, featureColour,
- start, end, y1);
-
+ start, end, y1, colourOnly);
+ if (drawn)
+ {
+ drawnColour = featureColour;
+ }
}
else if (showFeature(sequenceFeature))
{
- if (av_isShowSeqFeatureHeight
+ if (av.isShowSequenceFeaturesHeight()
&& !Float.isNaN(sequenceFeature.score))
{
- renderScoreFeature(g, seq,
+ boolean drawn = renderScoreFeature(g, seq,
seq.findIndex(sequenceFeature.begin) - 1,
- seq.findIndex(sequenceFeature.end) - 1,
- featureColour, start, end, y1,
- normaliseScore(sequenceFeature));
+ seq.findIndex(sequenceFeature.end) - 1, featureColour,
+ start, end, y1, normaliseScore(sequenceFeature),
+ colourOnly);
+ if (drawn)
+ {
+ drawnColour = featureColour;
+ }
}
else
{
- renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
- seq.findIndex(sequenceFeature.end) - 1,
- featureColour, start, end, y1);
+ boolean drawn = renderFeature(g, seq,
+ seq.findIndex(sequenceFeature.begin) - 1,
+ seq.findIndex(sequenceFeature.end) - 1, featureColour,
+ start, end, y1, colourOnly);
+ if (drawn)
+ {
+ drawnColour = featureColour;
+ }
}
}
}
if (transparency != 1.0f && g != null)
{
+ /*
+ * get colour as rendered including transparency
+ * and reset transparency
+ */
+ if (offscreenImage != null && drawnColour != null)
+ {
+ drawnColour = new Color(offscreenImage.getRGB(0, 0));
+ }
Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
- 1.0f));
+ g2.setComposite(NO_TRANSPARENCY);
}
+
+ return drawnColour;
}
/**
lastSeq = null;
findAllFeatures();
}
+
+ /**
+ * Returns the sequence feature colour rendered at the given sequence
+ * position, or null if none found. The feature of highest render order (i.e.
+ * on top) is found, subject to both feature type and feature group being
+ * visible, and its colour returned.
+ *
+ * @param seq
+ * @param pos
+ * @return
+ */
+ Color findFeatureColour(SequenceI seq, int pos)
+ {
+ SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
+ if (sequenceFeatures == null || sequenceFeatures.length == 0)
+ {
+ return null;
+ }
+
+ // updateFeatures();
+
+ /*
+ * inspect features in reverse renderOrder (the last in the array is
+ * displayed on top) until we find one that is rendered at the position
+ */
+ for (int renderIndex = renderOrder.length - 1; renderIndex >= 0; renderIndex--)
+ {
+ String type = renderOrder[renderIndex];
+ if (!showFeatureOfType(type))
+ {
+ continue;
+ }
+
+ for (int sfindex = 0; sfindex < sequenceFeatures.length; sfindex++)
+ {
+ SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
+ if (!sequenceFeature.type.equals(type))
+ {
+ continue;
+ }
+
+ if (featureGroupNotShown(sequenceFeature))
+ {
+ continue;
+ }
+
+ boolean featureIsAtPosition = sequenceFeature.begin <= pos
+ && sequenceFeature.end >= pos;
+ if (sequenceFeature.isContactFeature())
+ {
+ featureIsAtPosition = sequenceFeature.begin == pos
+ || sequenceFeature.end == pos;
+ }
+ if (featureIsAtPosition)
+ {
+ return getColour(sequenceFeature);
+ }
+ }
+ }
+
+ /*
+ * no displayed feature found at position
+ */
+ return null;
+ }
}
*/
package jalview.structures.models;
-import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
public abstract void setBackgroundColour(Color col);
protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI alignViewportI);
-
- /**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment);
+ String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
/**
* returns the current sequenceRenderer that should be used to colour the
SequenceRenderer sr = getSequenceRenderer(alignmentv);
- FeatureRenderer fr = null;
- boolean showFeatures = alignmentv.getAlignViewport()
- .isShowSequenceFeatures();
- if (showFeatures)
- {
- fr = getFeatureRenderer(alignmentv);
- }
-
StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
- files, sr, fr, alignmentv.getAlignViewport());
+ files, sr, alignmentv);
colourBySequence(colourBySequenceCommands);
}
{
return fileLoadingError != null && fileLoadingError.length() > 0;
}
+
+ protected abstract jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment);
}
* @return list of groups
*/
@Override
- public List getGroups(boolean visible)
+ public List<String> getGroups(boolean visible)
{
if (featureGroups != null)
{
// need some mappings!
StructureMappingcommandSet[] commands = JmolCommands
- .getColourBySequenceCommand(ssm, files, seqs, sr, null,
- af.getViewport());
+ .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
}
}
ssm.addStructureMapping(sm2);
StructureMappingcommandSet[] commands = ChimeraCommands
- .getColourBySequenceCommand(ssm, files, seqs, sr, null,
- af.getViewport());
+ .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
assertEquals(1, commands.length);
assertEquals(1, commands[0].commands.length);
String theCommand = commands[0].commands[0];
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
@Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
- {
- return null;
- }
-
- @Override
- public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ String[] files, SequenceRenderer sr, AlignmentViewPanel avp)
{
return null;
}
public void colourByCharge()
{
}
+
+ @Override
+ protected FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
+ {
+ return null;
+ }
};
}
git://source.jalview.org / jalview.git / commitdiff