ASX-TURN-IIL a67c98
BETA-TURN-IIR c79792
PHOSPHORYLATION (T) c88395
-BETA-TURN-IIL 8b5b50
-ST-MOTIF ac25a1
+BETA-TURN-IIL label
+#8b5b50
+ST-MOTIF label|||0|0
+#ac25a1
STARTGROUP uniprot
+ <html><a href="http://pfam.xfam.org/family/PF00111">Pfam family</a></html> FER_CAPAA -1 0 0 Pfam
Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_CAPAA -1 8 83 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html> FER_CAPAA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath
Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER_CAPAN -1 55 130 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_13</a></html> FER_CAPAN -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER_CAPAN -1 45 140 Cath
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> FER1_SOLLC -1 55 130 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_13</a></html> FER1_SOLLC -1 55 130 Pfam
Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 55_13</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 55_13</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
Ferredoxin_fold Status: True Positive Q93XJ9_SOLTU -1 45 140 Cath
Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_PEA -1 60 135 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html> FER1_PEA -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 63_13</a></html> Q7XA98_TRIPR -1 63 138 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 63_13</a></html> Q7XA98_TRIPR -1 63 138 Pfam
Ferredoxin_fold Status: True Positive Q7XA98_TRIPR -1 53 148 Cath
Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 59_13</a></html> FER1_MESCR -1 59 134 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 59_13</a></html> FER1_MESCR -1 59 134 Pfam
Ferredoxin_fold Status: True Positive FER1_MESCR -1 49 144 Cath
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 58_13</a></html> FER1_SPIOL -1 58 133 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 58_13</a></html> FER1_SPIOL -1 58 133 Pfam
Ferredoxin_fold Status: True Positive FER1_SPIOL -1 48 143 Cath
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER3_RAPSA -1 8 83 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html> FER3_RAPSA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER3_RAPSA -1 3 93 Cath
Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 8_8</a></html> FER_BRANA -1 8 83 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html> FER_BRANA -1 8 83 Pfam
Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath
Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER2_ARATH -1 60 135 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html> FER2_ARATH -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_11</a></html> Q93Z60_ARATH -1 60 118 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_11</a></html> Q93Z60_ARATH -1 60 118 Pfam
Ferredoxin_fold Status: True Positive Q93Z60_ARATH -1 52 118 Cath
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 60_13</a></html> FER1_MAIZE -1 60 135 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html> FER1_MAIZE -1 60 135 Pfam
Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath
- <html>Fer2 Status: True Positive <a href="http://pfam.sanger.ac.uk/family/PF00111">Pfam 52_12</a></html> O80429_MAIZE -1 52 127 Pfam
+ <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 52_12</a></html> O80429_MAIZE -1 52 127 Pfam
Ferredoxin_fold Status: True Positive O80429_MAIZE -1 42 137 Cath
ENDGROUP uniprot
*/
package MCview;
+import jalview.api.ColorI;
+import jalview.schemes.Colour;
import jalview.schemes.ResidueProperties;
-import java.awt.Color;
-
public class Atom
{
public float x;
public int type;
- Color color = Color.lightGray;
+ ColorI color = Colour.lightGray;
public String chain;
chain = str.substring(21, 22);
resNumber = Integer.parseInt(str.substring(22, 26).trim());
- resNumIns = str.substring(22, 27);
+ resNumIns = str.substring(22, 27).trim();
insCode = str.substring(26, 27).charAt(0);
this.x = (new Float(str.substring(30, 38).trim()).floatValue());
this.y = (new Float(str.substring(38, 46).trim()).floatValue());
}
}
+ @Override
+ public boolean equals(Object that)
+ {
+ if (this == that || that == null)
+ {
+ return true;
+ }
+ if (that instanceof Atom)
+ {
+ Atom other = (Atom) that;
+ return other.resName.equals(this.resName)
+ && other.resNumber == this.resNumber
+ && other.resNumIns.equals(this.resNumIns)
+ && other.chain.equals(this.chain);
+ }
+ return false;
+ }
public Atom(float x, float y, float z)
{
this.x = x;
package MCview;
import jalview.analysis.AlignSeq;
+import jalview.api.ColorI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.schemes.Colour;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
+ import jalview.structure.StructureImportSettings;
import jalview.structure.StructureMapping;
- import jalview.structure.StructureViewSettings;
import java.awt.Color;
import java.util.List;
public PDBChain(String pdbid, String id)
{
- this.pdbid = pdbid.toLowerCase();
+ this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase();
this.id = id;
}
else
{
- // boolean baseDetected = false;
- // for (Atom resAtom : resAtoms)
- // {
- // if (resAtom.insCode == ' ')
- // {
- // baseDetected = true;
- // }
- // }
- // if (!baseDetected)
- // {
- // continue;
- // }
// Make a new Residue object with the new atoms vector
residues.addElement(new Residue(resAtoms, resNumber - 1, count));
SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
+ ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
+ count, offset + count, pdbid);
- // MCview.PDBChain.PDBFILEFEATURE);
resFeatures.addElement(sf);
resAnnotation.addElement(new Annotation(tmpat.tfactor));
// Keep totting up the sequence
// System.out.println("PDB Sequence is :\nSequence = " + seq);
// System.out.println("No of residues = " + residues.size());
- if (StructureViewSettings.isShowSeqFeatures())
+ if (StructureImportSettings.isShowSeqFeatures())
{
for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
{
}
else
{
- b.startCol = Color.gray;
- b.endCol = Color.gray;
+ b.startCol = Colour.gray;
+ b.endCol = Colour.gray;
}
}
}
- public static Color getChargeColour(String resName)
+ public static ColorI getChargeColour(String resName)
{
- Color result = Color.lightGray;
+ ColorI result = Colour.lightGray;
if ("ASP".equals(resName) || "GLU".equals(resName))
{
- result = Color.red;
+ result = Colour.red;
}
else if ("LYS".equals(resName) || "ARG".equals(resName))
{
- result = Color.blue;
+ result = Colour.blue;
}
else if ("CYS".equals(resName))
{
- result = Color.yellow;
+ result = Colour.yellow;
}
return result;
}
try
{
index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
- b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+ b.startCol = new Colour(cs.findColour(ResidueProperties.aa[index]
+ .charAt(0)));
index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
- b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+ b.endCol = new Colour(cs.findColour(ResidueProperties.aa[index]
+ .charAt(0)));
} catch (Exception e)
{
- b.startCol = Color.gray;
- b.endCol = Color.gray;
+ b.startCol = Colour.gray;
+ b.endCol = Colour.gray;
}
}
}
{
for (Bond b : bonds)
{
- b.startCol = col;
- b.endCol = col;
+ b.startCol = new Colour(col);
+ b.endCol = new Colour(col);
}
}
{
for (AlignmentAnnotation ana : sequence.getAnnotation())
{
- List<AlignmentAnnotation> transfer = sq
+ List<AlignmentAnnotation> transfer = dsq
.getAlignmentAnnotations(ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
ana.liftOver(dsq, sqmpping);
+ dsq.addAlignmentAnnotation(ana);
// mapping.transfer(ana);
}
else
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
-import java.awt.Color;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
*/
public int calcPanelHeight();
+ /**
+ * Answers true if the viewport has at least one column selected
+ *
+ * @return
+ */
+ boolean hasSelectedColumns();
+
+ /**
+ * Answers true if the viewport has at least one hidden column
+ *
+ * @return
+ */
boolean hasHiddenColumns();
boolean isValidCharWidth();
void updateGroupAnnotationSettings(boolean applyGlobalSettings,
boolean preserveNewGroupSettings);
- void setSequenceColour(SequenceI seq, Color col);
+ void setSequenceColour(SequenceI seq, ColorI col);
- Color getSequenceColour(SequenceI seq);
+ ColorI getSequenceColour(SequenceI seq);
void updateSequenceIdColours();
* This method returns the visible alignment as text, as seen on the GUI, ie
* if columns are hidden they will not be returned in the result. Use this for
* calculating trees, PCA, redundancy etc on views which contain hidden
+ * columns. This method doesn't exclude hidden sequences from the output.
+ *
+ * @param selectedRegionOnly
+ * - determines if only the selected region or entire alignment is
+ * exported
+ * @return String[]
+ */
+ String[] getViewAsString(boolean selectedRegionOnly);
+
+ /**
+ * This method returns the visible alignment as text, as seen on the GUI, ie
+ * if columns are hidden they will not be returned in the result. Use this for
+ * calculating trees, PCA, redundancy etc on views which contain hidden
* columns.
*
+ * @param selectedRegionOnly
+ * - determines if only the selected region or entire alignment is
+ * exported
+ * @param isExportHiddenSeqs
+ * - determines if hidden sequences would be exported or not.
+ *
* @return String[]
*/
- String[] getViewAsString(boolean selectedRegionOnly);
+ String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);
void setSelectionGroup(SequenceGroup sg);
*/
void setFollowHighlight(boolean b);
+
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+ /**
+ * check if current selection group is defined on the view, or is simply a
+ * temporary group.
+ *
+ * @return true if group is defined on the alignment
+ */
+ boolean isSelectionDefinedGroup();
}
import jalview.datamodel.SequenceFeature;
-import java.awt.Color;
-
public interface FeatureColourI
{
/**
- * Answers true when either isColourByLabel, isAboveThreshold or
- * isBelowThreshold answers true
+ * Answers true when the feature colour varies across the score range
*
* @return
*/
*
* @return
*/
- Color getColour();
+ ColorI getColour();
/**
* Returns the minimum colour (when isGraduatedColour answers true)
*
* @return
*/
- Color getMinColour();
+ ColorI getMinColour();
/**
* Returns the maximum colour (when isGraduatedColour answers true)
*
* @return
*/
- Color getMaxColour();
+ ColorI getMaxColour();
/**
- * Answers true if the feature is coloured by label (description); only
- * applicable when isGraduatedColour answers true
+ * Answers true if the feature has a single colour, i.e. if isColourByLabel()
+ * and isGraduatedColour() both answer false
+ *
+ * @return
+ */
+ boolean isSimpleColour();
+
+ /**
+ * Answers true if the feature is coloured by label (description)
*
* @return
*/
boolean isColourByLabel();
+ void setColourByLabel(boolean b);
+
/**
* Answers true if the feature is coloured below a threshold value; only
* applicable when isGraduatedColour answers true
*/
boolean isBelowThreshold();
+ void setBelowThreshold(boolean b);
+
/**
* Answers true if the feature is coloured above a threshold value; only
* applicable when isGraduatedColour answers true
*/
boolean isAboveThreshold();
+ void setAboveThreshold(boolean b);
+
/**
- * Answers true if the threshold is the min (or max) of the colour range; only
- * applicable when isGraduatedColour answers true
+ * Answers true if the threshold is the minimum value (when
+ * isAboveThreshold()) or maximum value (when isBelowThreshold()) of the
+ * colour range; only applicable when isGraduatedColour and either
+ * isAboveThreshold() or isBelowThreshold() answers true
*
* @return
*/
boolean isThresholdMinMax();
+ void setThresholdMinMax(boolean b);
+
/**
* Returns the threshold value (if any), else zero
*
*/
float getThreshold();
- float getMax();
-
- /**
- * Returns the minimum score of the graduated colour range
- *
- * @return
- */
- float getMin();
+ void setThreshold(float f);
/**
+ * Answers true if either isAboveThreshold or isBelowThreshold answers true
+ *
+ * @return
+ */
+ boolean hasThreshold();
+
+ /**
- * Returns the computed colour for the given sequence feature
+ * Answers true if the colour varies between the actual minimum and maximum
+ * score values of the feature, or false if between absolute minimum and
+ * maximum values (or if not a graduated colour).
*
- * @param feature
* @return
*/
- ColorI getColor(SequenceFeature feature);
+ boolean isAutoScaled();
+
+ void setAutoScaled(boolean b);
/**
- * Returns the maximum score of the graduated colour range
+ * Answers true if the feature has a simple colour, or is coloured by label,
+ * or has a graduated colour and the score of this feature instance is within
+ * the range to render (if any), i.e. does not lie below or above any
+ * threshold set.
*
+ * @param feature
* @return
*/
- float getMax();
+ boolean isColored(SequenceFeature feature);
/**
- * Returns the minimum score of the graduated colour range
+ * Update the min-max range for a graduated colour scheme
*
- * @return
+ * @param min
+ * @param max
*/
- float getMin();
+ void updateBounds(float min, float max);
/**
- * Answers true if either isAboveThreshold or isBelowThreshold answers true
+ * Returns the colour in Jalview features file format
*
* @return
*/
- boolean hasThreshold();
+ String toJalviewFormat(String featureType);
- void setThreshold(float f);
-
- boolean isAutoScaled();
-
- void setAutoScaled(boolean b);
-
- boolean isSimpleColour();
-
- void setAboveThreshold(boolean b);
-
- void setThresholdMinMax(boolean b);
-
- void setBelowThreshold(boolean b);
+ /**
- * Returns the computed colour for the given sequence feature
++ * Returns the maximum score of the graduated colour range
+ *
- * @param feature
+ * @return
+ */
- Color getColor(SequenceFeature feature);
++ float getMax();
- void setColourByLabel(boolean b);
+ /**
- * Answers true if the feature has a simple colour, or is coloured by label,
- * or has a graduated colour and the score of this feature instance is within
- * the range to render (if any), i.e. does not lie below or above any
- * threshold set.
++ * Returns the minimum score of the graduated colour range
+ *
- * @param feature
+ * @return
+ */
- boolean isColored(SequenceFeature feature);
-
- /**
- * Update the min-max range for a graduated colour scheme
- *
- * @param min
- * @param max
- */
- void updateBounds(float min, float max);
++ float getMin();
- void setGraduatedColour(boolean b);
+ /**
- * Returns the colour in Jalview features file format
++ * Returns the computed colour for the given sequence feature
+ *
++ * @param feature
+ * @return
+ */
- String toJalviewFormat(String featureType);
++ ColorI getColor(SequenceFeature feature);
}
}
threshold.addItem(MessageManager
- .getString("label.threshold_feature_no_thereshold"));
+ .getString("label.threshold_feature_no_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_thereshold"));
+ .getString("label.threshold_feature_above_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_thereshold"));
+ .getString("label.threshold_feature_below_threshold"));
if (oldcs instanceof AnnotationColourGradient)
{
default:
throw new Error(
MessageManager
- .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
+ .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient"));
}
thresholdIsMin.setState(acg.thresholdIsMinMax);
thresholdValue.setText("" + acg.getAnnotationThreshold());
Checkbox thresholdIsMin = new Checkbox();
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == thresholdValue)
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == currentColours)
changeColour();
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
if (!adjusting)
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
ap.paintAlignment(true);
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
import jalview.api.FeatureColourI;
import jalview.datamodel.GraphLine;
import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.Colour;
import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.Checkbox;
Color bl = Color.black;
if (oldcs.isSimpleColour())
{
- bl = oldcs.getColour();
+ bl = ColorUtils.getColor(oldcs.getColour());
}
// original colour becomes the maximum colour
- cs = new FeatureColour(Color.white, bl, mm[0], mm[1]);
+ cs = new FeatureColour(new Colour(Color.white), new Colour(bl),
+ mm[0], mm[1]);
}
- minColour.setBackground(cs.getMinColour());
- maxColour.setBackground(cs.getMaxColour());
- minColour.setForeground(cs.getMinColour());
- maxColour.setForeground(cs.getMaxColour());
+ minColour.setBackground(ColorUtils.getColor(cs.getMinColour()));
+ maxColour.setBackground(ColorUtils.getColor(cs.getMaxColour()));
+ minColour.setForeground(ColorUtils.getColor(cs.getMinColour()));
+ maxColour.setForeground(ColorUtils.getColor(cs.getMaxColour()));
colourFromLabel.setState(cs.isColourByLabel());
adjusting = true;
jPanel4.setBackground(Color.white);
threshold.addItemListener(this);
threshold.addItem(MessageManager
- .getString("label.threshold_feature_no_thereshold"));
+ .getString("label.threshold_feature_no_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_thereshold"));
+ .getString("label.threshold_feature_above_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_thereshold"));
+ .getString("label.threshold_feature_below_threshold"));
thresholdValue.addActionListener(this);
slider.setBackground(Color.white);
slider.setEnabled(false);
// ap.paintAlignment(false);
}
- public void minColour_actionPerformed(Color newCol)
+ public void minColour_actionPerformed(Color c)
{
- if (newCol == null)
+ if (c == null)
{
UserDefinedColours udc = new UserDefinedColours(this,
minColour.getBackground(), owner,
}
else
{
- minColour.setBackground(newCol);
- minColour.setForeground(newCol);
+ minColour.setBackground(c);
+ minColour.setForeground(c);
minColour.repaint();
changeColour();
}
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- FeatureColour acg = new FeatureColour(minColour.getBackground(),
- maxColour.getBackground(), min, max);
+ FeatureColour acg = new FeatureColour(new Colour(
+ minColour.getBackground()), new Colour(
+ maxColour.getBackground()), min, max);
acg.setColourByLabel(colourFromLabel.getState());
maxColour.setEnabled(!colourFromLabel.getState());
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.FeaturesFile;
+import jalview.schemes.Colour;
import jalview.schemes.FeatureColour;
import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
public class FeatureRenderer extends
jalview.renderer.seqfeatures.FeatureRenderer
{
- /**
- * Creates a new FeatureRenderer object.
- *
- * @param av
- * DOCUMENT ME!
- */
- public FeatureRenderer(AlignmentViewport av)
- {
- super();
- this.av = av;
- }
-
+ // Holds web links for feature groups and feature types
+ // in the form label|link
+ Hashtable featureLinks = null;
- /**
- * Creates a new FeatureRenderer object.
- *
- * @param av
- */
- public FeatureRenderer(AlignmentViewport av)
- {
- super(av);
-
- }
-
static String lastFeatureAdded;
static String lastFeatureGroupAdded;
FeatureColourPanel colourPanel;
++ /**
++ * Creates a new FeatureRenderer object.
++ *
++ * @param av
++ */
++ public FeatureRenderer(AlignmentViewport av)
++ {
++ super(av);
++ }
++
class FeatureColourPanel extends Panel
{
String label = "";
String vlabel = "";
if (newcol.isSimpleColour())
{
- bg = newcol.getColour();
+ bg = ColorUtils.getColor(newcol.getColour());
setBackground(bg);
}
else
}
else
{
- setBackground(bg = newcol.getMinColour());
- maxCol = newcol.getMaxColour();
+ setBackground(bg = ColorUtils.getColor(newcol.getMinColour()));
+ maxCol = ColorUtils.getColor(newcol.getMaxColour());
}
}
label = vlabel;
{
Color generatedColour = UserColourScheme
.createColourFromName(name.getText());
- col = new FeatureColour(generatedColour);
+ col = new FeatureColour(new Colour(generatedColour));
}
colourPanel.updateColor(col);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label("Name: ", Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT));
tmp.add(name);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label("Group: ", Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT));
tmp.add(source);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label("Colour: ", Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT));
tmp.add(colourPanel);
bigPanel.add(panel, BorderLayout.NORTH);
panel = new Panel();
- panel.add(new Label("Description: ", Label.RIGHT));
+ panel.add(new Label(MessageManager.getString("label.description:"),
+ Label.RIGHT));
panel.add(new ScrollPane().add(description));
if (!newFeatures)
bigPanel.add(panel, BorderLayout.SOUTH);
panel = new Panel();
- panel.add(new Label(" Start:", Label.RIGHT));
+ panel.add(new Label(MessageManager.getString("label.start"),
+ Label.RIGHT));
panel.add(start);
- panel.add(new Label(" End:", Label.RIGHT));
+ panel.add(new Label(MessageManager.getString("label.end"),
+ Label.RIGHT));
panel.add(end);
bigPanel.add(panel, BorderLayout.CENTER);
}
if (!colourPanel.isGcol)
{
// update colour - otherwise its already done.
- setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
+ setColour(
+ sf.type,
+ new FeatureColour(new Colour(colourPanel.getBackground())));
}
try
{
{
setGroupVisibility(lastFeatureGroupAdded, true);
}
- setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol
+ setColour(lastFeatureAdded,
+ new FeatureColour(new Colour(newColour))); // was fcol
setVisible(lastFeatureAdded);
findAllFeatures(false); // different to original applet behaviour ?
// findAllFeatures();
import jalview.api.FeatureSettingsControllerI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
final FeatureColourI typeCol = fr.getFeatureStyle(type);
PopupMenu men = new PopupMenu(MessageManager.formatMessage(
"label.settings_for_type", new String[] { type }));
- java.awt.MenuItem scr = new MenuItem(
+ MenuItem scr = new MenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
final FeatureSettings me = this;
FeatureColourI fcol = fr.getFeatureStyle(check.type);
if (fcol.isSimpleColour())
{
- new UserDefinedColours(this, check.type, fcol.getColour());
+ new UserDefinedColours(this, check.type, ColorUtils.getColor(fcol
+ .getColour()));
}
else
{
col = newcol;
if (col.isSimpleColour())
{
- setBackground(col.getColour());
+ setBackground(ColorUtils.getColor(col.getColour()));
}
else
{
}
else
{
- setBackground(col.getMinColour());
+ setBackground(ColorUtils.getColor(col.getMinColour()));
}
this.setLabel(vlabel);
}
public void paint(Graphics g)
{
Dimension d = getSize();
- if (col.isColourByLabel())
+ if (col != null)
{
- g.setColor(Color.white);
- g.fillRect(d.width / 2, 0, d.width / 2, d.height);
- /*
- * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
- * g.setFont(f);
- *
- * // g.setFont(g.getFont().deriveFont( //
- * AffineTransform.getScaleInstance( //
- * width/g.getFontMetrics().stringWidth("Label"), //
- * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
- * width/2, 0);
- */
-
- }
- else if (col.isGraduatedColour())
- {
- Color maxCol = ColorUtils.getColor(col.getMaxColour());
- g.setColor(maxCol);
- g.fillRect(d.width / 2, 0, d.width / 2, d.height);
-
+ if (col.isColourByLabel())
+ {
+ g.setColor(Color.white);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ /*
+ * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
+ * g.setFont(f);
+ *
+ * // g.setFont(g.getFont().deriveFont( //
+ * AffineTransform.getScaleInstance( //
+ * width/g.getFontMetrics().stringWidth("Label"), //
+ * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
+ * width/2, 0);
+ */
-
+ }
+ else if (col.isGraduatedColour())
+ {
- Color maxCol = col.getMaxColour();
++ Color maxCol = ColorUtils.getColor(col.getMaxColour());
+ g.setColor(maxCol);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
-
+ }
}
if (hasLink)
}
}
- @Override
- public void mousePressed(MouseEvent e)
- {
- }
-
/**
* Hide columns containing (or not containing) a given feature type
*
}
}
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
}
package jalview.appletgui;
import jalview.datamodel.AlignmentI;
+import jalview.util.ColorUtils;
import java.awt.Color;
import java.awt.Dimension;
{
miniMe = null;
int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getHeight();
+ int alheight = av.getAlignment().getHeight()
+ + av.getAlignment().getHiddenSequences().getSize();
if (av.isShowSequenceFeatures())
{
AlignmentI alignment = av.getAlignment();
for (row = 0; row <= sequencesHeight; row++)
{
+ if (resizeAgain)
+ {
+ break;
+ }
if ((int) (row * sampleRow) == lastrow)
{
sameRow++;
if (seq.getLength() > lastcol)
{
- color = sr.getResidueBoxColour(seq, lastcol);
+ color = ColorUtils.getColor(sr.getResidueBoxColour(seq, lastcol));
if (av.isShowSequenceFeatures())
{
- color = fr.findFeatureColour(color, seq, lastcol);
+ color = ColorUtils.getColor(fr.findFeatureColour(color, seq,
+ lastcol));
}
}
else
{
for (col = 0; col < width; col++)
{
+ if (resizeAgain)
+ {
+ break;
+ }
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+ import jalview.renderer.ScaleRenderer;
+ import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.util.ColorUtils;
import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
- int scalestartx = startx - startx % 10 + 10;
-
+ updateViewport();
g.setColor(Color.black);
-
- // NORTH SCALE
- for (int i = scalestartx; i < endx; i += 10)
+ for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+ endx))
{
- int value = i;
- if (av.hasHiddenColumns())
+ int mpos = mark.column; // (i - startx - 1)
+ if (mpos < 0)
{
- value = av.getColumnSelection().adjustForHiddenColumns(value);
+ continue;
}
+ String mstring = mark.text;
- g.drawString(String.valueOf(value), (i - startx - 1) * avcharWidth,
- ypos - (avcharHeight / 2));
-
- g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
- (ypos + 2) - (avcharHeight / 2),
- ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
- ypos - 2);
+ if (mark.major)
+ {
+ if (mstring != null)
+ {
+ g.drawString(mstring, mpos * avcharWidth, ypos
+ - (avcharHeight / 2));
+ }
+ g.drawLine((mpos * avcharWidth) + (avcharWidth / 2), (ypos + 2)
+ - (avcharHeight / 2), (mpos * avcharWidth)
+ + (avcharWidth / 2),
+ ypos - 2);
+ }
}
}
}
else
{
- g.setColor(group.getOutlineColour());
+ g.setColor(ColorUtils.getColor(group.getOutlineColour()));
}
}
}
*/
package jalview.appletgui;
+import jalview.api.ColorI;
import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.schemes.Colour;
import jalview.schemes.ColourSchemeI;
import java.awt.Color;
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
+ final static int CHAR_TO_UPPER = 'A' - 'a';
+
AlignViewport av;
FontMetrics fm;
}
@Override
- public Color getResidueBoxColour(SequenceI seq, int i)
+ public ColorI getResidueBoxColour(SequenceI seq, int i)
{
allGroups = av.getAlignment().findAllGroups(seq);
getBoxColour(av.getGlobalColourScheme(), seq, i);
}
- return resBoxColour;
+ return new Colour(resBoxColour);
}
/**
* @return
*/
@Override
- public Color getResidueColour(final SequenceI seq, int position,
+ public ColorI getResidueColour(final SequenceI seq, int position,
FeatureRenderer fr)
{
// TODO replace 8 or so code duplications with calls to this method
// (refactored as needed)
- Color col = getResidueBoxColour(seq, position);
+ ColorI col = getResidueBoxColour(seq, position);
if (fr != null)
{
}
if (currentSequenceGroup.getShowNonconserved())
{
- s = getDisplayChar(srep, i, s, '.');
+ s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
}
}
else
}
if (av.getShowUnconserved())
{
- s = getDisplayChar(srep, i, s, '.');
+ s = getDisplayChar(srep, i, s, '.', null);
}
}
}
- private char getDisplayChar(final boolean usesrep, int position, char s,
- char c)
+ /**
+ * Returns 'conservedChar' to represent the given position if the sequence
+ * character at that position is equal to the consensus (ignoring case), else
+ * returns the sequence character
+ *
+ * @param usesrep
+ * @param position
+ * @param sequenceChar
+ * @param conservedChar
+ * @return
+ */
+ private char getDisplayChar(final boolean usesrep, int position,
+ char sequenceChar, char conservedChar, SequenceGroup currentGroup)
{
// TODO - use currentSequenceGroup rather than alignment
// currentSequenceGroup.getConsensus()
- char conschar = (usesrep) ? av.getAlignment().getSeqrep()
- .getCharAt(position)
- : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
- .charAt(0);
- if (!jalview.util.Comparison.isGap(conschar) && s == conschar)
+ char conschar = (usesrep) ? (currentGroup == null
+ || position < currentGroup.getStartRes()
+ || position > currentGroup.getEndRes() ? av.getAlignment()
+ .getSeqrep().getCharAt(position)
+ : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
+ .getCharAt(position) : av.getAlignment().getSeqrep()
+ .getCharAt(position)))
+ : (currentGroup != null && currentGroup.getConsensus() != null
+ && position >= currentGroup.getStartRes()
+ && position <= currentGroup.getEndRes() && currentGroup
+ .getConsensus().annotations.length > position) ? currentGroup
+ .getConsensus().annotations[position].displayCharacter
+ .charAt(0)
+ : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+ .charAt(0);
+ if (!jalview.util.Comparison.isGap(conschar)
+ && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
{
- s = c;
+ sequenceChar = conservedChar;
}
- return s;
+ return sequenceChar;
}
boolean inCurrentSequenceGroup(int res)
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
+import jalview.schemes.Colour;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import jalview.util.Format;
import jalview.util.MappingUtils;
import jalview.viewmodel.AlignmentViewport;
tree.findHeight(tree.getTopNode());
// Now have to calculate longest name based on the leaves
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+ Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
boolean has_placeholders = false;
longestName = "";
for (int i = 0; i < leaves.size(); i++)
{
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+ SequenceNode lf = leaves.elementAt(i);
if (lf.isPlaceholder())
{
}
else
{
- g.setColor(av.getSequenceColour(seq).darker());
+ g.setColor(ColorUtils.getColor(av.getSequenceColour(seq))
+ .darker());
}
}
if (node.element() instanceof SequenceI)
{
- av.setSequenceColour((SequenceI) node.element(), c);
+ av.setSequenceColour((SequenceI) node.element(), new Colour(c));
}
}
else
}
else
{
- Vector leaves = new Vector();
- tree.findLeaves(highlightNode, leaves);
+ Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
for (int i = 0; i < leaves.size(); i++)
{
- SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
+ SequenceI seq = (SequenceI) leaves.elementAt(i)
.element();
treeSelectionChanged(seq);
}
(int) (Math.random() * 255), (int) (Math.random() * 255));
setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
- Vector l = tree.findLeaves(
- (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+ Vector<SequenceNode> l = tree.findLeaves((SequenceNode) tree
+ .getGroups().elementAt(i));
- Vector sequences = new Vector();
+ Vector<SequenceI> sequences = new Vector<SequenceI>();
for (int j = 0; j < l.size(); j++)
{
- SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
+ SequenceI s1 = (SequenceI) l.elementAt(j)
.element();
if (!sequences.contains(s1))
{
for (SequenceI seq : mappedGroup.getSequences())
{
// TODO why does gui require col.brighter() here??
- codingComplement.setSequenceColour(seq, col);
+ codingComplement.setSequenceColour(seq, new Colour(col));
}
}
}
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.ColorI;
import jalview.api.FeatureRenderer;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.FeaturesFile;
+import jalview.schemes.Colour;
import jalview.util.MessageManager;
import java.awt.Color;
viewport.getAlignment().addGroup(gps[g]);
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
+ ColorI newcol = new Colour(col.brighter());
for (SequenceI sq : gps[g].getSequences(null))
{
- viewport.setSequenceColour(sq, col);
+ viewport.setSequenceColour(sq, newcol);
}
}
return true;
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
BitSet bs = new BitSet();
- int alw, alStart;
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
- .getAlignment() : viewport.getSelectionGroup());
- alStart = sqcol.getStartRes();
- alw = sqcol.getEndRes() + 1;
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
+ .getAlignment() : viewport.getSelectionGroup();
+
+ int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(true);
+ int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
+ : bs.cardinality();
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked",
+ new String[] {
+ toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
+ featureType, Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.no_feature_of_type_found",
+ new String[] { featureType }));
+ if (!extendCurrent)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(true);
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Sets a bit in the BitSet for each column (base 0) in the sequence
+ * collection which includes the specified feature type. Returns the number of
+ * sequences which have the feature in the selected range.
+ *
+ * @param featureType
+ * @param sqcol
+ * @param bs
+ * @return
+ */
+ static int findColumnsWithFeature(String featureType,
+ SequenceCollectionI sqcol, BitSet bs)
+ {
+ final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
+ final int endPosition = sqcol.getEndRes() + 1;
List<SequenceI> seqs = sqcol.getSequences();
int nseq = 0;
for (SequenceI sq : seqs)
{
- int tfeat = 0;
+ boolean sequenceHasFeature = false;
if (sq != null)
{
- SequenceFeature[] sf = sq.getSequenceFeatures();
- if (sf != null)
+ SequenceFeature[] sfs = sq.getSequenceFeatures();
+ if (sfs != null)
{
+ /*
+ * check whether the feature start/end (base 1)
+ * overlaps the selection start/end
+ */
int ist = sq.findIndex(sq.getStart());
int iend = sq.findIndex(sq.getEnd());
- if (iend < alStart || ist > alw)
+ if (iend < startPosition || ist > endPosition)
{
// sequence not in region
continue;
}
- for (SequenceFeature sfpos : sf)
+ for (SequenceFeature sf : sfs)
{
- // future functionalty - featureType == null means mark columns
+ // future functionality - featureType == null means mark columns
// containing all displayed features
- if (sfpos != null && (featureType.equals(sfpos.getType())))
+ if (sf != null && (featureType.equals(sf.getType())))
{
- tfeat++;
// optimisation - could consider 'spos,apos' like cursor argument
// - findIndex wastes time by starting from first character and
// counting
- int i = sq.findIndex(sfpos.getBegin());
- int j = sq.findIndex(sfpos.getEnd());
- if (j < alStart || i > alw)
+ int i = sq.findIndex(sf.getBegin());
+ int j = sq.findIndex(sf.getEnd());
+ if (j < startPosition || i > endPosition)
{
// feature is outside selected region
continue;
}
- if (i < alStart)
+ sequenceHasFeature = true;
+ if (i < startPosition)
{
- i = alStart;
+ i = startPosition;
}
if (i < ist)
{
i = ist;
}
- if (j > alw)
+ if (j > endPosition)
{
- j = alw;
+ j = endPosition;
}
for (; i <= j; i++)
{
- bs.set(i - 1);
+ bs.set(i - 1); // convert to base 0
}
}
}
}
- if (tfeat > 0)
+ if (sequenceHasFeature)
{
nseq++;
}
}
}
- ColumnSelection cs = viewport.getColumnSelection();
- if (bs.cardinality() > 0 || invert)
- {
- boolean changed = false;
- if (cs == null)
- {
- cs = new ColumnSelection();
- }
- else
- {
- if (!extendCurrent)
- {
- changed = !cs.isEmpty();
- cs.clear();
- }
- }
- if (invert)
- {
- // invert only in the currently selected sequence region
- for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
- && i < (alw);)
- {
- if (ibs < 0 || i < ibs)
- {
- changed = true;
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i++);
- }
- else
- {
- cs.addElement(i++);
- }
- }
- else
- {
- i = bs.nextClearBit(ibs);
- ibs = bs.nextSetBit(i);
- }
- }
- }
- else
- {
- for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
- .nextSetBit(i + 1))
- {
- changed = true;
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i);
- }
- else
- {
- cs.addElement(i);
- }
- }
- }
- if (changed)
- {
- viewport.setColumnSelection(cs);
- alignPanel.paintAlignment(true);
- avcg.setStatus(MessageManager.formatMessage(
- "label.view_controller_toggled_marked",
- new String[] {
- (toggle ? MessageManager.getString("label.toggled")
- : MessageManager.getString("label.marked")),
- (invert ? (Integer.valueOf((alw - alStart)
- - bs.cardinality()).toString()) : (Integer
- .valueOf(bs.cardinality()).toString())),
- featureType, Integer.valueOf(nseq).toString() }));
- return true;
- }
- }
- else
- {
- avcg.setStatus(MessageManager.formatMessage(
- "label.no_feature_of_type_found",
- new String[] { featureType }));
- if (!extendCurrent && cs != null)
- {
- cs.clear();
- alignPanel.paintAlignment(true);
- }
- }
- return false;
+ return nseq;
}
@Override
import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
+import jalview.api.ColorI;
+import jalview.schemes.Colour;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
// end column (base 0)
int endRes = 0;
- public Color outlineColour = Color.black;
+ public ColorI outlineColour = Colour.black;
- public Color idColour = null;
+ public ColorI idColour = null;
public int thresholdTextColour = 0;
- public Color textColour = Color.black;
+ public ColorI textColour = Colour.black;
- public Color textColour2 = Color.white;
+ public ColorI textColour2 = Colour.white;
/**
* consensus calculation property
}
/**
- * calculate residue conservation for group - but only if necessary.
+ * calculate residue conservation and colourschemes for group - but only if
+ * necessary. returns true if the calculation resulted in a visible change to
+ * group
*/
- public void recalcConservation()
+ public boolean recalcConservation()
+ {
+ return recalcConservation(false);
+ }
+
+ /**
+ * calculate residue conservation for group - but only if necessary. returns
+ * true if the calculation resulted in a visible change to group
+ *
+ * @param defer
+ * when set, colourschemes for this group are not refreshed after
+ * recalculation
+ */
+ public boolean recalcConservation(boolean defer)
{
if (cs == null && consensus == null && conservation == null)
{
- return;
+ return false;
}
+ // TODO: try harder to detect changes in state in order to minimise
+ // recalculation effort
+ boolean upd = false;
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
if (consensus != null)
{
_updateConsensusRow(cnsns, sequences.size());
+ upd = true;
}
if (cs != null)
{
cs.setConsensus(cnsns);
+ upd = true;
}
if ((conservation != null)
cs.setConservation(c);
}
}
+ // eager update - will cause a refresh of overview regardless
+ upd = true;
}
- if (cs != null)
+ if (cs != null && !defer)
{
+ // TODO: JAL-2034 should cs.alignmentChanged modify return state
cs.alignmentChanged(context != null ? context : this, null);
+ return true;
+ }
+ else
+ {
+ return upd;
}
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
System.out.println("Out of memory loading groups: " + err);
}
-
+ return upd;
}
private void _updateConservationRow(Conservation c)
*/
public void setOutlineColour(Color c)
{
- outlineColour = c;
+ outlineColour = new Colour(c);
}
/**
*
* @return DOCUMENT ME!
*/
- public Color getOutlineColour()
+ public ColorI getOutlineColour()
{
return outlineColour;
}
/**
* @return the idColour
*/
- public Color getIdColour()
+ public ColorI getIdColour()
{
return idColour;
}
*/
public void setIdColour(Color idColour)
{
- this.idColour = idColour;
+ this.idColour = new Colour(idColour);
}
/**
/**
*
- * @return automatically calculated consensus row
+ * @return automatically calculated consensus row note: the row is a stub if a
+ * consensus calculation has not yet been performed on the group
*/
public AlignmentAnnotation getConsensus()
{
package jalview.ext.ensembl;
+import jalview.api.ColorI;
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
-import jalview.schemes.FeatureColour;
+import jalview.schemes.Colour;
+import jalview.schemes.FeatureColourAdapter;
import jalview.schemes.FeatureSettingsAdapter;
import jalview.util.MapList;
-import java.awt.Color;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.util.ArrayList;
* fetch the gene sequence(s) with features and xrefs
*/
AlignmentI geneAlignment = super.getSequenceRecords(geneId);
-
+ if (geneAlignment == null)
+ {
+ continue;
+ }
if (geneAlignment.getHeight() == 1)
{
getTranscripts(geneAlignment, geneId);
*/
else
{
- List<String> ids = new EnsemblSymbol(getDomain()).getIds(acc);
+ List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
+ getDbVersion()).getIds(acc);
for (String geneId : ids)
{
if (!geneIds.contains(geneId))
*/
protected String getGeneIdentifiersForName(String query)
{
- List<String> ids = new EnsemblSymbol(getDomain()).getIds(query);
+ List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
+ getDbVersion()).getIds(query);
if (ids != null)
{
for (String id : ids)
{
if (so.isA(type, SequenceOntologyI.EXON))
{
- return new FeatureColour()
+ return new FeatureColourAdapter()
{
@Override
public boolean isColourByLabel()
}
if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
{
- return new FeatureColour()
+ return new FeatureColourAdapter()
{
@Override
- public Color getColour()
+ public ColorI getColour()
{
- return Color.RED;
+ return Colour.red;
}
};
}
import jalview.math.AlignmentDimension;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
}
else
{
- currentColor = av.getSequenceColour(seq);
+ currentColor = ColorUtils.getColor(av.getSequenceColour(seq));
currentTextColor = Color.black;
}
void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
{
+ int boarderBottomOffset = 5;
long pSessionId = System.currentTimeMillis();
headless = (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true"));
}
im = new jalview.util.ImageMaker(this, type, imageAction,
- aDimension.getWidth(), aDimension.getHeight(), file,
+ aDimension.getWidth(), aDimension.getHeight()
+ + boarderBottomOffset, file,
imageTitle, alignFrame, pSessionId, headless);
if (av.getWrapAlignment())
{
if (im.getGraphics() != null)
{
printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
- aDimension.getHeight(), 0);
+ aDimension.getHeight() + boarderBottomOffset, 0);
im.writeImage();
}
}
import jalview.api.FeatureColourI;
import jalview.datamodel.GraphLine;
+import jalview.schemes.Colour;
import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
else
{
// promote original color to a graduated color
- Color bl = oldcs.getColour();
+ Color bl = ColorUtils.getColor(oldcs.getColour());
if (bl == null)
{
bl = Color.BLACK;
}
// original colour becomes the maximum colour
- cs = new FeatureColour(Color.white, bl, mm[0], mm[1]);
+ cs = new FeatureColour(new Colour(Color.white), new Colour(bl),
+ mm[0], mm[1]);
cs.setColourByLabel(false);
}
- minColour.setBackground(oldminColour = cs.getMinColour());
- maxColour.setBackground(oldmaxColour = cs.getMaxColour());
+ minColour.setBackground(oldminColour = ColorUtils.getColor(cs
+ .getMinColour()));
+ maxColour.setBackground(oldmaxColour = ColorUtils.getColor(cs
+ .getMaxColour()));
adjusting = true;
try
threshold.setToolTipText(MessageManager
.getString("label.threshold_feature_display_by_score"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_no_thereshold")); // index 0
+ .getString("label.threshold_feature_no_threshold")); // index 0
threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_thereshold")); // index 1
+ .getString("label.threshold_feature_above_threshold")); // index 1
threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_thereshold")); // index 2
+ .getString("label.threshold_feature_below_threshold")); // index 2
jPanel3.setLayout(flowLayout2);
thresholdValue.addActionListener(new ActionListener()
{
slider.setOpaque(false);
slider.setPreferredSize(new Dimension(100, 32));
slider.setToolTipText(MessageManager
- .getString("label.adjust_thereshold"));
+ .getString("label.adjust_threshold"));
thresholdValue.setEnabled(false);
thresholdValue.setColumns(7);
jPanel3.setBackground(Color.white);
FeatureColourI acg;
if (cs.isColourByLabel())
{
- acg = new FeatureColour(oldminColour, oldmaxColour, min, max);
+ acg = new FeatureColour(new Colour(oldminColour), new Colour(
+ oldmaxColour), min, max);
}
else
{
- acg = new FeatureColour(oldminColour = minColour.getBackground(),
- oldmaxColour = maxColour.getBackground(), min, max);
-
+ acg = new FeatureColour(new Colour(
+ oldminColour = minColour.getBackground()), new Colour(
+ oldmaxColour = maxColour.getBackground()), min, max);
-
}
if (!hasThreshold)
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.schemes.Colour;
import jalview.schemes.FeatureColour;
import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
*/
public FeatureRenderer(AlignmentPanel ap)
{
- super();
+ super(ap.av);
this.ap = ap;
- this.av = ap.av;
if (ap != null && ap.getSeqPanel() != null
&& ap.getSeqPanel().seqCanvas != null
&& ap.getSeqPanel().seqCanvas.fr != null)
{
Color col = JColorChooser.showDialog(Desktop.desktop,
MessageManager.getString("label.select_feature_colour"),
- fcol.getColour());
+ ColorUtils.getColor(fcol.getColour()));
if (col != null)
{
- fcol = new FeatureColour(col);
- updateColourButton(bigPanel, colour, new FeatureColour(col));
+ fcol = new FeatureColour(new Colour(col));
+ updateColourButton(bigPanel, colour, fcol);
}
}
else
{
panel = new JPanel(new GridLayout(4, 1));
tmp = new JPanel();
- tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
+ tmp.add(new JLabel(MessageManager.getString("label.select_feature")
+ + ":"));
overlaps = new JComboBox();
for (int i = 0; i < features.length; i++)
{
FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- col = new FeatureColour(UserColourScheme
- .createColourFromName(name.getText()));
+ col = new FeatureColour(new Colour(UserColourScheme
+ .createColourFromName(name.getText())));
}
oldcol = fcol = col;
updateColourButton(bigPanel, colour, col);
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
+ tmp.add(new JLabel(MessageManager.getString("label.name:"),
+ JLabel.RIGHT));
tmp.add(name);
tmp = new JPanel();
panel.add(tmp);
- tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
+ tmp.add(new JLabel(MessageManager.getString("label.group:"),
JLabel.RIGHT));
tmp.add(source);
bigPanel.add(panel, BorderLayout.NORTH);
panel = new JPanel();
- panel.add(new JLabel(MessageManager.getString("label.description"),
+ panel.add(new JLabel(MessageManager.getString("label.description:"),
JLabel.RIGHT));
description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
* update the amend feature button dependent on the given style
*
* @param bigPanel
+ * @param colour
* @param col
++<<<<<<< HEAD
++=======
+ * @param col
++>>>>>>> refs/heads/develop
*/
protected void updateColourButton(JPanel bigPanel, JLabel colour,
FeatureColourI col)
if (col.isSimpleColour())
{
- colour.setBackground(col.getColour());
+ colour.setBackground(ColorUtils.getColor(col.getColour()));
}
else
{
import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
import jalview.schemabinding.version2.JalviewUserColours;
+import jalview.schemes.Colour;
import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
import jalview.util.Format;
import jalview.util.MessageManager;
import jalview.util.Platform;
}
else if (evt.getClickCount() == 2)
{
+ boolean invertSelection = evt.isAltDown();
+ boolean toggleSelection = Platform.isControlDown(evt);
+ boolean extendSelection = evt.isShiftDown();
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
- evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(),
- evt.isMetaDown(),
+ invertSelection, extendSelection, toggleSelection,
(String) table.getValueAt(selectedRow, 0));
}
}
- // isPopupTrigger fires on mouseReleased on Mac
+ // isPopupTrigger fires on mouseReleased on Windows
@Override
public void mouseReleased(MouseEvent evt)
{
int newRow = table.rowAtPoint(evt.getPoint());
if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
{
+ /*
+ * reposition 'selectedRow' to 'newRow' (the dragged to location)
+ * this could be more than one row away for a very fast drag action
+ * so just swap it with adjacent rows until we get it there
+ */
Object[][] data = ((FeatureTableModel) table.getModel())
.getData();
- Object[] temp = data[selectedRow];
- data[selectedRow] = data[newRow];
- data[newRow] = temp;
+ int direction = newRow < selectedRow ? -1 : 1;
+ for (int i = selectedRow; i != newRow; i += direction)
+ {
+ Object[] temp = data[i];
+ data[i] = data[i + direction];
+ data[i + direction] = temp;
+ }
updateFeatureRenderer(data);
table.repaint();
selectedRow = newRow;
"Select new Colour", true, // modal
colorChooser, this, // OK button handler
null); // no CANCEL button handler
- colorChooser.setColor(featureColour.getMaxColour());
+ colorChooser.setColor(ColorUtils.getColor(featureColour
+ .getMaxColour()));
dialog.setVisible(true);
}
}
else
{
// probably the color chooser!
- table.setValueAt(colorChooser.getColor(), selectedRow, 1);
+ table.setValueAt(
+ new FeatureColour(colorChooser.getColor()),
+ selectedRow, 1);
table.validate();
me.updateFeatureRenderer(
((FeatureTableModel) table.getModel()).getData(),
Cache.log.warn("Couldn't parse out graduated feature color.",
e);
}
- FeatureColourI gcol = new FeatureColour(mincol, maxcol,
+ FeatureColourI gcol = new FeatureColour(new Colour(mincol),
+ new Colour(maxcol),
newcol.getMin(), newcol.getMax());
if (newcol.hasAutoScale())
{
Color color = new Color(
Integer.parseInt(jucs.getColour(i).getRGB(), 16));
fr.setColour(name = jucs.getColour(i).getName(),
- new FeatureColour(color));
+ new FeatureColour(new Colour(color)));
}
fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
}
void save()
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ Cache.getProperty("LAST_DIRECTORY"),
new String[] { "fc" },
new String[] { "Sequence Feature Colours" },
"Sequence Feature Colours");
{
this.setText("");
this.setIcon(null);
- newColor = cellColour.getColour();
+ newColor = ColorUtils.getColor(cellColour.getColour());
setBackground(newColor);
- // comp.setToolTipText("RGB value: " + newColor.getRed() + ", "
- // + newColor.getGreen() + ", " + newColor.getBlue());
}
if (isSelected)
{
}
else
{
- Color newColor = gcol.getMaxColour();
+ Color newColor = ColorUtils.getColor(gcol.getMaxColour());
comp.setBackground(newColor);
// System.err.println("Width is " + w / 2);
Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
g.setColor(backg);
g.fillRect(0, 0, width, height);
// need an icon here.
- g.setColor(gcol.getMaxColour());
+ g.setColor(ColorUtils.getColor(gcol.getMaxColour()));
g.setFont(new Font("Verdana", Font.PLAIN, 9));
}
else
{
- Color minCol = gcol.getMinColour();
+ Color minCol = ColorUtils.getColor(gcol.getMinColour());
g.setColor(minCol);
g.fillRect(0, 0, s1, height);
if (midspace)
g.setColor(Color.white);
g.fillRect(s1, 0, e1 - s1, height);
}
- g.setColor(gcol.getMaxColour());
+ g.setColor(ColorUtils.getColor(gcol.getMaxColour()));
g.fillRect(0, e1, width - e1, height);
}
}
if (currentColor.isSimpleColour())
{
// bring up simple color chooser
- button.setBackground(currentColor.getColour());
- colorChooser.setColor(currentColor.getColour());
+ button.setBackground(ColorUtils.getColor(currentColor.getColour()));
+ colorChooser
+ .setColor(ColorUtils.getColor(currentColor.getColour()));
dialog.setVisible(true);
}
else
{ // User pressed dialog's "OK" button.
if (currentColor.isSimpleColour())
{
- currentColor = new FeatureColour(colorChooser.getColor());
+ currentColor = new FeatureColour(
+ new Colour(colorChooser.getColor()));
}
else
{
{
button.setText("");
button.setIcon(null);
- button.setBackground(currentColor.getColour());
+ button.setBackground(ColorUtils.getColor(currentColor.getColour()));
}
return button;
}
import jalview.schemabinding.version2.UserColours;
import jalview.schemabinding.version2.Viewport;
import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.Colour;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.FeatureColour;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
import jalview.util.Platform;
+ import jalview.util.StringUtils;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
+ import java.util.Arrays;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
- import java.util.StringTokenizer;
import java.util.Vector;
import java.util.jar.JarEntry;
import java.util.jar.JarInputStream;
*/
Map<String, SequenceI> seqRefIds = null;
- Vector<Object[]> frefedSequence = null;
+ Map<String, SequenceI> incompleteSeqs = null;
+
+ List<SeqFref> frefedSequence = null;
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
{
seqsToIds.clear();
}
+ if (incompleteSeqs != null)
+ {
+ incompleteSeqs.clear();
+ }
// seqRefIds = null;
// seqsToIds = null;
}
{
seqRefIds = new HashMap<String, SequenceI>();
}
+ if (incompleteSeqs == null)
+ {
+ incompleteSeqs = new HashMap<String, SequenceI>();
+ }
+ if (frefedSequence == null)
+ {
+ frefedSequence = new ArrayList<SeqFref>();
+ }
}
public Jalview2XML()
this.raiseGUI = raiseGUI;
}
- public void resolveFrefedSequences()
+ /**
+ * base class for resolving forward references to sequences by their ID
+ *
+ * @author jprocter
+ *
+ */
+ abstract class SeqFref
{
- if (frefedSequence.size() > 0)
+ String sref;
+
+ String type;
+
+ public SeqFref(String _sref, String type)
+ {
+ sref = _sref;
+ this.type = type;
+ }
+
+ public String getSref()
+ {
+ return sref;
+ }
+
+ public SequenceI getSrefSeq()
+ {
+ return seqRefIds.get(sref);
+ }
+
+ public boolean isResolvable()
+ {
+ return seqRefIds.get(sref) != null;
+ }
+
+ public SequenceI getSrefDatasetSeq()
{
- int r = 0, rSize = frefedSequence.size();
- while (r < rSize)
+ SequenceI sq = seqRefIds.get(sref);
+ if (sq != null)
{
- Object[] ref = frefedSequence.elementAt(r);
- if (ref != null)
+ while (sq.getDatasetSequence() != null)
{
- String sref = (String) ref[0];
- if (seqRefIds.containsKey(sref))
- {
- if (ref[1] instanceof jalview.datamodel.Mapping)
- {
- SequenceI seq = seqRefIds.get(sref);
- while (seq.getDatasetSequence() != null)
- {
- seq = seq.getDatasetSequence();
- }
- ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
- }
- else
- {
- if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
- {
- SequenceI seq = seqRefIds.get(sref);
- while (seq.getDatasetSequence() != null)
- {
- seq = seq.getDatasetSequence();
- }
- if (ref[2] != null
- && ref[2] instanceof jalview.datamodel.Mapping)
- {
- jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
- ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
- seq, mp.getTo(), mp.getMap());
- }
- else
- {
- System.err
- .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
- + ref[2].getClass() + " type objects.");
- }
- }
- else
- {
- System.err
- .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
- + ref[1].getClass() + " type objects.");
- }
- }
- frefedSequence.remove(r);
- rSize--;
- }
- else
+ sq = sq.getDatasetSequence();
+ }
+ }
+ return sq;
+ }
+ /**
+ * @return true if the forward reference was fully resolved
+ */
+ abstract boolean resolve();
+
+ @Override
+ public String toString()
+ {
+ return type + " reference to " + sref;
+ }
+ }
+
+ /**
+ * create forward reference for a mapping
+ *
+ * @param sref
+ * @param _jmap
+ * @return
+ */
+ public SeqFref newMappingRef(final String sref,
+ final jalview.datamodel.Mapping _jmap)
+ {
+ SeqFref fref = new SeqFref(sref, "Mapping")
+ {
+ public jalview.datamodel.Mapping jmap = _jmap;
+
+ @Override
+ boolean resolve()
+ {
+ SequenceI seq = getSrefDatasetSeq();
+ if (seq == null)
+ {
+ return false;
+ }
+ jmap.setTo(seq);
+ return true;
+ }
+ };
+ return fref;
+ }
+
+ public SeqFref newAlcodMapRef(final String sref,
+ final AlignedCodonFrame _cf, final jalview.datamodel.Mapping _jmap)
+ {
+
+ SeqFref fref = new SeqFref(sref, "Codon Frame")
+ {
+ AlignedCodonFrame cf = _cf;
+
+ public jalview.datamodel.Mapping mp = _jmap;
+
+ @Override
+ public boolean isResolvable()
+ {
+ return super.isResolvable() && mp.getTo() != null;
+ };
+
+ @Override
+ boolean resolve()
+ {
+ SequenceI seq = getSrefDatasetSeq();
+ if (seq == null)
+ {
+ return false;
+ }
+ cf.addMap(seq, mp.getTo(), mp.getMap());
+ return true;
+ }
+ };
+ return fref;
+ }
+
+ public void resolveFrefedSequences()
+ {
+ Iterator<SeqFref> nextFref=frefedSequence.iterator();
+ int toresolve=frefedSequence.size();
+ int unresolved=0,failedtoresolve=0;
+ while (nextFref.hasNext()) {
+ SeqFref ref = nextFref.next();
+ if (ref.isResolvable())
+ {
+ try {
+ if (ref.resolve())
{
- System.err
- .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
- + ref[0]
- + " with objecttype "
- + ref[1].getClass());
- r++;
+ nextFref.remove();
+ } else {
+ failedtoresolve++;
}
- }
- else
+ } catch (Exception x) {
+ System.err.println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "+ref.getSref());
+ x.printStackTrace();
+ failedtoresolve++;
+ }
+ } else {
+ unresolved++;
+ }
+ }
+ if (unresolved>0)
+ {
+ System.err.println("Jalview Project Import: There were " + unresolved
+ + " forward references left unresolved on the stack.");
+ }
+ if (failedtoresolve>0)
+ {
+ System.err.println("SERIOUS! " + failedtoresolve
+ + " resolvable forward references failed to resolve.");
+ }
+ if (incompleteSeqs != null && incompleteSeqs.size() > 0)
+ {
+ System.err.println("Jalview Project Import: There are "
+ + incompleteSeqs.size()
+ + " sequences which may have incomplete metadata.");
+ if (incompleteSeqs.size() < 10)
+ {
+ for (SequenceI s : incompleteSeqs.values())
{
- // empty reference
- frefedSequence.remove(r);
- rSize--;
+ System.err.println(s.toString());
}
}
+ else
+ {
+ System.err
+ .println("Too many to report. Skipping output of incomplete sequences.");
+ }
}
}
{
return;
}
+ saveAllFrames(Arrays.asList(frames), jout);
+ }
+ /**
+ * core method for storing state for a set of AlignFrames.
+ *
+ * @param frames
+ * - frames involving all data to be exported (including containing
+ * splitframes)
+ * @param jout
+ * - project output stream
+ */
+ private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
+ {
Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
/*
List<String> viewIds = new ArrayList<String>();
// REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
+ for (int i = frames.size() - 1; i > -1; i--)
{
- AlignFrame af = frames[i];
+ AlignFrame af = frames.get(i);
// skip ?
if (skipList != null
&& skipList
{
try
{
- int ap = 0;
- int apSize = af.alignPanels.size();
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
- Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
- List<String> viewIds = new ArrayList<String>();
+ List<AlignFrame> frames = new ArrayList<AlignFrame>();
- for (AlignmentPanel apanel : af.alignPanels)
+ // resolve splitframes
+ if (af.getViewport().getCodingComplement() != null)
{
- String jfileName = apSize == 1 ? fileName : fileName + ap;
- ap++;
- if (!jfileName.endsWith(".xml"))
- {
- jfileName = jfileName + ".xml";
- }
- saveState(apanel, jfileName, jout, viewIds);
- String dssid = getDatasetIdRef(af.getViewport().getAlignment()
- .getDataset());
- if (!dsses.containsKey(dssid))
- {
- dsses.put(dssid, af);
- }
+ frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
+ }
+ else
+ {
+ frames.add(af);
}
- writeDatasetFor(dsses, fileName, jout);
+ saveAllFrames(frames, jout);
try
{
jout.flush();
object.setVersion(jalview.bin.Cache.getDefault("VERSION",
"Development Build"));
- jalview.datamodel.AlignmentI jal = av.getAlignment();
+ /**
+ * rjal is full height alignment, jal is actual alignment with full metadata
+ * but excludes hidden sequences.
+ */
+ jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
if (av.hasHiddenRows())
{
- jal = jal.getHiddenSequences().getFullAlignment();
+ rjal = jal.getHiddenSequences().getFullAlignment();
}
SequenceSet vamsasSet = new SequenceSet();
{
// switch jal and the dataset
jal = jal.getDataset();
+ rjal = jal;
}
}
if (jal.getProperties() != null)
JSeq jseq;
Set<String> calcIdSet = new HashSet<String>();
-
+ // record the set of vamsas sequence XML POJO we create.
+ HashMap<String,Sequence> vamsasSetIds = new HashMap<String,Sequence>();
// SAVE SEQUENCES
- for (int i = 0; i < jal.getHeight(); i++)
+ for (final SequenceI jds : rjal.getSequences())
{
final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
: jds.getDatasetSequence();
String id = seqHash(jds);
-
- if (seqRefIds.get(id) != null)
- {
- // This happens for two reasons: 1. multiple views are being serialised.
- // 2. the hashCode has collided with another sequence's code. This DOES
- // HAPPEN! (PF00072.15.stk does this)
- // JBPNote: Uncomment to debug writing out of files that do not read
- // back in due to ArrayOutOfBoundExceptions.
- // System.err.println("vamsasSeq backref: "+id+"");
- // System.err.println(jds.getName()+"
- // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(jds));
- // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
- // System.err.println(rsq.getName()+"
- // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(rsq));
- }
- else
- {
- vamsasSeq = createVamsasSequence(id, jds);
- vamsasSet.addSequence(vamsasSeq);
- seqRefIds.put(id, jds);
+ if (vamsasSetIds.get(id) == null)
+ {
+ if (seqRefIds.get(id) != null && !storeDS)
+ {
+ // This happens for two reasons: 1. multiple views are being
+ // serialised.
+ // 2. the hashCode has collided with another sequence's code. This
+ // DOES
+ // HAPPEN! (PF00072.15.stk does this)
+ // JBPNote: Uncomment to debug writing out of files that do not read
+ // back in due to ArrayOutOfBoundExceptions.
+ // System.err.println("vamsasSeq backref: "+id+"");
+ // System.err.println(jds.getName()+"
+ // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(jds));
+ // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
+ // System.err.println(rsq.getName()+"
+ // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(rsq));
+ }
+ else
+ {
+ vamsasSeq = createVamsasSequence(id, jds);
+ vamsasSet.addSequence(vamsasSeq);
+ vamsasSetIds.put(id, vamsasSeq);
+ seqRefIds.put(id, jds);
+ }
}
-
jseq = new JSeq();
jseq.setStart(jds.getStart());
jseq.setEnd(jds.getEnd());
// Store any sequences this sequence represents
if (av.hasHiddenRows())
{
+ // use rjal, contains the full height alignment
jseq.setHidden(av.getAlignment().getHiddenSequences()
.isHidden(jds));
- if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
+ if (av.isHiddenRepSequence(jds))
{
jalview.datamodel.SequenceI[] reps = av
- .getRepresentedSequences(jal.getSequenceAt(i))
- .getSequencesInOrder(jal);
+ .getRepresentedSequences(jds)
+ .getSequencesInOrder(rjal);
for (int h = 0; h < reps.length; h++)
{
- if (reps[h] != jal.getSequenceAt(i))
+ if (reps[h] != jds)
{
- jseq.addHiddenSequences(jal.findIndex(reps[h]));
+ jseq.addHiddenSequences(rjal.findIndex(reps[h]));
}
}
}
}
+ // mark sequence as reference - if it is the reference for this view
+ if (jal.hasSeqrep())
+ {
+ jseq.setViewreference(jds == jal.getSeqrep());
+ }
}
+ // TODO: omit sequence features from each alignment view's XML dump if we
+ // are storing dataset
if (jds.getSequenceFeatures() != null)
{
jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
jal = av.getAlignment();
}
// SAVE MAPPINGS
- if (jal.getCodonFrames() != null)
+ // FOR DATASET
+ if (storeDS && jal.getCodonFrames() != null)
{
List<AlignedCodonFrame> jac = jal.getCodonFrames();
for (AlignedCodonFrame acf : jac)
{
AlcodonFrame alc = new AlcodonFrame();
if (acf.getProtMappings() != null
&& acf.getProtMappings().length > 0)
{
+ boolean hasMap = false;
SequenceI[] dnas = acf.getdnaSeqs();
jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
for (int m = 0; m < pmaps.length; m++)
alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
false));
alc.addAlcodMap(alcmap);
+ hasMap = true;
+ }
+ if (hasMap)
+ {
+ vamsasSet.addAlcodonFrame(alc);
}
}
-
+ // TODO: delete this ? dead code from 2.8.3->2.9 ?
// {
// AlcodonFrame alc = new AlcodonFrame();
// vamsasSet.addAlcodonFrame(alc);
Vector<String> settingsAdded = new Vector<String>();
if (renderOrder != null)
{
- for (int ro = 0; ro < renderOrder.length; ro++)
+ for (String featureType : renderOrder)
{
- FeatureColourI gstyle = ap.getSeqPanel().seqCanvas
+ FeatureColourI fcol = ap.getSeqPanel().seqCanvas
.getFeatureRenderer()
- .getFeatureStyle(renderOrder[ro]);
+ .getFeatureStyle(featureType);
Setting setting = new Setting();
- setting.setType(renderOrder[ro]);
- if (!gstyle.isSimpleColour())
+ setting.setType(featureType);
+ if (!fcol.isSimpleColour())
{
- setting.setColour(gstyle.getMaxColour().getRGB());
- setting.setMincolour(gstyle.getMinColour().getRGB());
- setting.setMin(gstyle.getMin());
- setting.setMax(gstyle.getMax());
- setting.setColourByLabel(gstyle.isColourByLabel());
- setting.setAutoScale(gstyle.isAutoScaled());
- setting.setThreshold(gstyle.getThreshold());
+ setting.setColour(fcol.getMaxColour().getRGB());
+ setting.setMincolour(fcol.getMinColour().getRGB());
+ setting.setMin(fcol.getMin());
+ setting.setMax(fcol.getMax());
+ setting.setColourByLabel(fcol.isColourByLabel());
+ setting.setAutoScale(fcol.isAutoScaled());
+ setting.setThreshold(fcol.getThreshold());
// -1 = No threshold, 0 = Below, 1 = Above
- setting.setThreshstate(gstyle.isAboveThreshold() ? 1
- : (gstyle.isBelowThreshold() ? 0 : -1));
+ setting.setThreshstate(fcol.isAboveThreshold() ? 1
+ : (fcol.isBelowThreshold() ? 0 : -1));
}
else
{
- setting.setColour(gstyle.getColour().getRGB());
+ setting.setColour(fcol.getColour().getRGB());
}
setting.setDisplay(av.getFeaturesDisplayed().isVisible(
- renderOrder[ro]));
+ featureType));
float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getOrder(renderOrder[ro]);
+ .getOrder(featureType);
if (rorder > -1)
{
setting.setOrder(rorder);
}
fs.addSetting(setting);
- settingsAdded.addElement(renderOrder[ro]);
+ settingsAdded.addElement(featureType);
}
}
Vector<String> groupsAdded = new Vector<String>();
while (en.hasNext())
{
- String grp = en.next().toString();
+ String grp = en.next();
if (groupsAdded.contains(grp))
{
continue;
if (jds.getDatasetSequence() != null)
{
vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
}
else
{
- vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
+ // seqId==dsseqid so we can tell which sequences really are
// dataset sequences only
+ vamsasSeq.setDsseqid(id);
dbrefs = jds.getDBRefs();
+ if (parentseq == null)
+ {
+ parentseq = jds;
+ }
}
if (dbrefs != null)
{
if (jmp.getTo() != null)
{
MappingChoice mpc = new MappingChoice();
- if (recurse
- && (parentseq != jmp.getTo() || parentseq
- .getDatasetSequence() != jmp.getTo()))
+
+ // check/create ID for the sequence referenced by getTo()
+
+ String jmpid = "";
+ SequenceI ps = null;
+ if (parentseq != jmp.getTo()
+ && parentseq.getDatasetSequence() != jmp.getTo())
{
- mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
- jmp.getTo(), jds));
+ // chaining dbref rather than a handshaking one
+ jmpid = seqHash(ps = jmp.getTo());
}
else
{
- String jmpid = "";
- SequenceI ps = null;
- if (parentseq != jmp.getTo()
- && parentseq.getDatasetSequence() != jmp.getTo())
- {
- // chaining dbref rather than a handshaking one
- jmpid = seqHash(ps = jmp.getTo());
- }
- else
- {
- jmpid = seqHash(ps = parentseq);
- }
- mpc.setDseqFor(jmpid);
- if (!seqRefIds.containsKey(mpc.getDseqFor()))
- {
- jalview.bin.Cache.log.debug("creatign new DseqFor ID");
- seqRefIds.put(mpc.getDseqFor(), ps);
- }
- else
- {
- jalview.bin.Cache.log.debug("reusing DseqFor ID");
- }
+ jmpid = seqHash(ps = parentseq);
+ }
+ mpc.setDseqFor(jmpid);
+ if (!seqRefIds.containsKey(mpc.getDseqFor()))
+ {
+ jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+ seqRefIds.put(mpc.getDseqFor(), ps);
}
+ else
+ {
+ jalview.bin.Cache.log.debug("reusing DseqFor ID");
+ }
+
mp.setMappingChoice(mpc);
}
}
}
if (seqRefIds == null)
{
- seqRefIds = new HashMap<String, SequenceI>();
- }
- if (frefedSequence == null)
- {
- frefedSequence = new Vector<Object[]>();
+ initSeqRefs();
}
-
AlignFrame af = null, _af = null;
+ IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<AlignmentI, AlignmentI>();
Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
final String file = jprovider.getFilename();
try
if (true) // !skipViewport(object))
{
_af = loadFromObject(object, file, true, jprovider);
- if (object.getJalviewModelSequence().getViewportCount() > 0)
+ if (_af != null
+ && object.getJalviewModelSequence().getViewportCount() > 0)
{
- af = _af;
- if (af.viewport.isGatherViewsHere())
+ if (af == null)
+ {
+ // store a reference to the first view
+ af = _af;
+ }
+ if (_af.viewport.isGatherViewsHere())
{
- gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ // if this is a gathered view, keep its reference since
+ // after gathering views, only this frame will remain
+ af = _af;
+ gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af);
}
+ // Save dataset to register mappings once all resolved
+ importedDatasets.put(af.viewport.getAlignment().getDataset(),
+ af.viewport.getAlignment().getDataset());
}
}
entryCount++;
e.printStackTrace();
}
- if (Desktop.instance != null)
- {
- Desktop.instance.stopLoading();
- }
-
/*
* Regather multiple views (with the same sequence set id) to the frame (if
* any) that is flagged as the one to gather to, i.e. convert them to tabbed
}
restoreSplitFrames();
-
+ for (AlignmentI ds : importedDatasets.keySet())
+ {
+ if (ds.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerMappings(ds.getCodonFrames());
+ }
+ }
if (errorMessage != null)
{
reportErrors();
}
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+
return af;
}
* @param pdbId
* @return
*/
- String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
+ String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
+ String origFile)
{
if (alreadyLoadedPDB.containsKey(pdbId))
{
return alreadyLoadedPDB.get(pdbId).toString();
}
- String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb");
+ String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
+ origFile);
if (tempFile != null)
{
alreadyLoadedPDB.put(pdbId, tempFile);
* @param prefix
* a prefix for the temporary file name, must be at least three
* characters long
+ * @param origFile
+ * null or original file - so new file can be given the same suffix
+ * as the old one
* @return
*/
protected String copyJarEntry(jarInputStreamProvider jprovider,
- String jarEntryName, String prefix)
+ String jarEntryName, String prefix, String origFile)
{
BufferedReader in = null;
PrintWriter out = null;
-
+ String suffix = ".tmp";
+ if (origFile == null)
+ {
+ origFile = jarEntryName;
+ }
+ int sfpos = origFile.lastIndexOf(".");
+ if (sfpos > -1 && sfpos < (origFile.length() - 3))
+ {
+ suffix = "." + origFile.substring(sfpos + 1);
+ }
try
{
JarInputStream jin = jprovider.getJarInputStream();
if (entry != null)
{
in = new BufferedReader(new InputStreamReader(jin, UTF_8));
- File outFile = File.createTempFile(prefix, ".tmp");
+ File outFile = File.createTempFile(prefix, suffix);
outFile.deleteOnExit();
out = new PrintWriter(new FileOutputStream(outFile));
String data;
// LOAD SEQUENCES
List<SequenceI> hiddenSeqs = null;
- jalview.datamodel.Sequence jseq;
+
List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
boolean multipleView = false;
-
+ SequenceI referenceseqForView = null;
JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
int vi = 0; // counter in vamsasSeq array
for (int i = 0; i < jseqs.length; i++)
{
String seqId = jseqs[i].getId();
- if (seqRefIds.get(seqId) != null)
+ SequenceI tmpSeq = seqRefIds.get(seqId);
+ if (tmpSeq != null)
{
- tmpseqs.add(seqRefIds.get(seqId));
- multipleView = true;
+ if (!incompleteSeqs.containsKey(seqId))
+ {
+ // may not need this check, but keep it for at least 2.9,1 release
+ if (tmpSeq.getStart()!=jseqs[i].getStart() || tmpSeq.getEnd()!=jseqs[i].getEnd())
+ {
+ System.err
+ .println("Warning JAL-2154 regression: updating start/end for sequence "
+ + tmpSeq.toString() + " to " + jseqs[i]);
+ }
+ } else {
+ incompleteSeqs.remove(seqId);
+ }
+ if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
+ {
+ // most likely we are reading a dataset XML document so
+ // update from vamsasSeq section of XML for this sequence
+ tmpSeq.setName(vamsasSeq[vi].getName());
+ tmpSeq.setDescription(vamsasSeq[vi].getDescription());
+ tmpSeq.setSequence(vamsasSeq[vi].getSequence());
+ vi++;
+ }
+ else
+ {
+ // reading multiple views, so vamsasSeq set is a subset of JSeq
+ multipleView = true;
+ }
+ tmpSeq.setStart(jseqs[i].getStart());
+ tmpSeq.setEnd(jseqs[i].getEnd());
+ tmpseqs.add(tmpSeq);
}
else
{
- jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
+ tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
vamsasSeq[vi].getSequence());
- jseq.setDescription(vamsasSeq[vi].getDescription());
- jseq.setStart(jseqs[i].getStart());
- jseq.setEnd(jseqs[i].getEnd());
- jseq.setVamsasId(uniqueSetSuffix + seqId);
- seqRefIds.put(vamsasSeq[vi].getId(), jseq);
- tmpseqs.add(jseq);
+ tmpSeq.setDescription(vamsasSeq[vi].getDescription());
+ tmpSeq.setStart(jseqs[i].getStart());
+ tmpSeq.setEnd(jseqs[i].getEnd());
+ tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
+ seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
+ tmpseqs.add(tmpSeq);
vi++;
}
+ if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
+ {
+ referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
+ }
+
if (jseqs[i].getHidden())
{
if (hiddenSeqs == null)
hiddenSeqs = new ArrayList<SequenceI>();
}
- hiddenSeqs.add(seqRefIds.get(seqId));
+ hiddenSeqs.add(tmpSeq);
}
-
}
// /
SequenceI[] orderedSeqs = tmpseqs
.toArray(new SequenceI[tmpseqs.size()]);
- Alignment al = new Alignment(orderedSeqs);
-
- // / Add the alignment properties
- for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
- {
- SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
- al.setProperty(ssp.getKey(), ssp.getValue());
- }
-
- // /
- // SequenceFeatures are added to the DatasetSequence,
- // so we must create or recover the dataset before loading features
+ AlignmentI al = null;
+ // so we must create or recover the dataset alignment before going further
// ///////////////////////////////
if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
{
- // older jalview projects do not have a dataset id.
+ // older jalview projects do not have a dataset - so creat alignment and
+ // dataset
+ al = new Alignment(orderedSeqs);
al.setDataset(null);
}
else
{
- // recover dataset - passing on flag indicating if this a 'viewless'
- // sequence set (a.k.a. a stored dataset for the project)
- recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
- .getViewportCount() == 0);
+ boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0;
+ if (isdsal)
+ {
+ // we are importing a dataset record, so
+ // recover reference to an alignment already materialsed as dataset
+ al = getDatasetFor(vamsasSet.getDatasetId());
+ }
+ if (al == null)
+ {
+ // materialse the alignment
+ al = new Alignment(orderedSeqs);
+ }
+ if (isdsal)
+ {
+ addDatasetRef(vamsasSet.getDatasetId(), al);
+ }
+
+ // finally, verify all data in vamsasSet is actually present in al
+ // passing on flag indicating if it is actually a stored dataset
+ recoverDatasetFor(vamsasSet, al, isdsal);
+ }
+
+ if (referenceseqForView != null)
+ {
+ al.setSeqrep(referenceseqForView);
}
+ // / Add the alignment properties
+ for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
+ {
+ SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
+ al.setProperty(ssp.getKey(), ssp.getValue());
+ }
+
// ///////////////////////////////
Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
{
// load sequence features, database references and any associated PDB
// structures for the alignment
+ //
+ // prior to 2.10, this part would only be executed the first time a
+ // sequence was encountered, but not afterwards.
+ // now, for 2.10 projects, this is also done if the xml doc includes
+ // dataset sequences not actually present in any particular view.
+ //
for (int i = 0; i < vamsasSeq.length; i++)
{
if (jseqs[i].getFeaturesCount() > 0)
}
}
-
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+ // adds feature to datasequence's feature set (since Jalview 2.10)
+ al.getSequenceAt(i).addSequenceFeature(sf);
}
}
if (vamsasSeq[i].getDBRefCount() > 0)
{
- addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
+ // adds dbrefs to datasequence's set (since Jalview 2.10)
+ addDBRefs(
+ al.getSequenceAt(i).getDatasetSequence() == null ? al.getSequenceAt(i)
+ : al.getSequenceAt(i).getDatasetSequence(),
+ vamsasSeq[i]);
}
if (jseqs[i].getPdbidsCount() > 0)
{
entry.setId(ids[p].getId());
if (ids[p].getType() != null)
{
- if (ids[p].getType().equalsIgnoreCase("PDB"))
+ if (PDBEntry.Type.getType(ids[p].getType()) != null)
{
- entry.setType(PDBEntry.Type.PDB);
+ entry.setType(PDBEntry.Type.getType(ids[p].getType()));
}
else
{
{
if (!pdbloaded.containsKey(ids[p].getFile()))
{
- entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ entry.setFile(loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile()));
}
else
{
entry.setFile(pdbloaded.get(ids[p].getId()).toString());
}
}
+ if (ids[p].getPdbentryItem() != null)
+ {
+ entry.setProperty(new Hashtable());
+ for (PdbentryItem item : ids[p].getPdbentryItem())
+ {
+ for (Property pr : item.getProperty())
+ {
+ entry.getProperty().put(pr.getName(), pr.getValue());
+ }
+ }
+ }
StructureSelectionManager.getStructureSelectionManager(
Desktop.instance).registerPDBEntry(entry);
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ // adds PDBEntry to datasequence's set (since Jalview 2.10)
+ if (al.getSequenceAt(i).getDatasetSequence() != null)
+ {
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ }
+ else
+ {
+ al.getSequenceAt(i).addPDBId(entry);
+ }
}
}
}
if (maps[m].getMapping() != null)
{
mapping = addMapping(maps[m].getMapping());
- }
- if (dnaseq != null && mapping.getTo() != null)
- {
- cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
- }
- else
- {
- // defer to later
- frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
- mapping });
+ if (dnaseq != null && mapping.getTo() != null)
+ {
+ cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+ }
+ else
+ {
+ // defer to later
+ frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf,
+ mapping));
+ }
}
}
+ al.addCodonFrame(cf);
}
- al.addCodonFrame(cf);
}
}
sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
- sg.textColour = new java.awt.Color(jGroup.getTextCol1());
- sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
+ sg.textColour = new Colour(jGroup.getTextCol1());
+ sg.textColour2 = new Colour(jGroup.getTextCol2());
sg.setShowNonconserved(jGroup.hasShowUnconserved() ? jGroup
.isShowUnconserved() : false);
sg.thresholdTextColour = jGroup.getTextColThreshold();
String rnaTitle = ss.getTitle();
String sessionState = ss.getViewerState();
String tempStateFile = copyJarEntry(jprovider, sessionState,
- "varna");
+ "varna", null);
RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
appVarna.addModelSession(rna, rnaTitle, tempStateFile);
}
// Originally : ids[p].getFile()
// : TODO: verify external PDB file recovery still works in normal
// jalview project load
- jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile()));
jpdb.setId(ids[p].getId());
int x = structureState.getXpos();
// Probably don't need to do this anymore...
// Desktop.desktop.getComponentAt(x, y);
// TODO: NOW: check that this recovers the PDB file correctly.
- String pdbFile = loadPDBFile(jprovider, ids[p].getId());
+ String pdbFile = loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile());
jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
.getId() + "");
if (sviewid == null)
*/
String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
- "chimera");
+ "chimera", null);
Set<Entry<File, StructureData>> fileData = data.getFileData()
.entrySet();
// filename
// translation differently.
StructureData filedat = oldFiles.get(new File(oldfilenam));
+ if (filedat == null)
+ {
+ String reformatedOldFilename = oldfilenam.replaceAll("/",
+ "\\\\");
+ filedat = oldFiles.get(new File(reformatedOldFilename));
+ }
newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
pdbfilenames.add(filedat.getFilePath());
pdbids.add(filedat.getPdbId());
}
/**
+ * Answers true if 'version' is equal to or later than 'supported', where each
+ * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
+ * changes. Development and test values for 'version' are leniently treated
+ * i.e. answer true.
*
* @param supported
* - minimum version we are comparing against
* @param version
- * - version of data being processsed.
- * @return true if version is development/null or evaluates to the same or
- * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
+ * - version of data being processsed
+ * @return
*/
public static boolean isVersionStringLaterThan(String supported,
String version)
{
- if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
+ if (supported == null || version == null
+ || version.equalsIgnoreCase("DEVELOPMENT BUILD")
|| version.equalsIgnoreCase("Test")
|| version.equalsIgnoreCase("AUTOMATED BUILD"))
{
}
else
{
- StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer(
- version, ".");
- while (currentV.hasMoreTokens() && fileV.hasMoreTokens())
- {
- // convert b to decimal to catch bugfix releases within a series
- String curT = currentV.nextToken().toLowerCase().replace('b', '.');
- String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
- try
- {
- float supportedVersionToken = Float.parseFloat(curT);
- float myVersiontoken = Float.parseFloat(fileT);
- if (supportedVersionToken > myVersiontoken)
- {
- // current version is newer than the version that wrote the file
- return false;
- }
- if (supportedVersionToken < myVersiontoken)
- {
- // current version is older than the version that wrote the file
- return true;
- }
- } catch (NumberFormatException nfe)
- {
- System.err
- .println("** WARNING: Version comparison failed for tokens ("
- + curT
- + ") and ("
- + fileT
- + ")\n** Current: '"
- + supported + "' and Version: '" + version + "'");
- }
- }
- if (currentV.hasMoreElements())
- {
- // fileV has no minor version but identical series to current
- return false;
- }
+ return StringUtils.compareVersions(version, supported, "b") >= 0;
}
- return true;
}
Vector<JalviewStructureDisplayI> newStructureViewers = null;
}
AlignFrame loadViewport(String file, JSeq[] JSEQ,
- List<SequenceI> hiddenSeqs, Alignment al,
+ List<SequenceI> hiddenSeqs, AlignmentI al,
JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
String viewId, List<JvAnnotRow> autoAlan)
{
for (int i = 0; i < JSEQ.length; i++)
{
af.viewport.setSequenceColour(af.viewport.getAlignment()
- .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
+ .getSequenceAt(i), new Colour(JSEQ[i].getColour()));
}
+ if (al.hasSeqrep())
+ {
+ af.getViewport().setColourByReferenceSeq(true);
+ af.getViewport().setDisplayReferenceSeq(true);
+ }
+
af.viewport.setGatherViewsHere(view.getGatheredViews());
if (view.getSequenceSetId() != null)
{
for (int s = 0; s < JSEQ.length; s++)
{
- jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
-
+ SequenceGroup hidden = new SequenceGroup();
+ boolean isRepresentative = false;
for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
{
- hidden.addSequence(
- al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
+ isRepresentative = true;
+ SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s]
+ .getHiddenSequences(r));
+ hidden.addSequence(sequenceToHide, false);
+ // remove from hiddenSeqs list so we don't try to hide it twice
+ hiddenSeqs.remove(sequenceToHide);
+ }
+ if (isRepresentative)
+ {
+ SequenceI representativeSequence = al.getSequenceAt(s);
+ hidden.addSequence(representativeSequence, false);
+ af.viewport.hideRepSequences(representativeSequence, hidden);
}
- af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
}
- // jalview.datamodel.SequenceI[] hseqs = new
- // jalview.datamodel.SequenceI[hiddenSeqs
- // .size()];
- //
- // for (int s = 0; s < hiddenSeqs.size(); s++)
- // {
- // hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
- // }
-
SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
.size()]);
af.viewport.hideSequence(hseqs);
af.viewport.setShowText(view.getShowText());
- af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
- af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
+ af.viewport.setTextColour(new Colour(view.getTextCol1()));
+ af.viewport.setTextColour2(new Colour(view.getTextCol2()));
af.viewport.setThresholdTextColour(view.getTextColThreshold());
af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
.isShowUnconserved() : false);
if (setting.hasMincolour())
{
FeatureColourI gc = setting.hasMin() ? new FeatureColour(
- new Color(setting.getMincolour()), new Color(
- setting.getColour()), setting.getMin(),
- setting.getMax()) : new FeatureColour(new Color(
- setting.getMincolour()), new Color(setting.getColour()),
+ new Colour(new Color(setting.getMincolour())),
+ new Colour(new Color(setting.getColour())),
+ setting.getMin(), setting.getMax()) : new FeatureColour(
+ new Colour(new Color(setting.getMincolour())),
+ new Colour(new Color(setting.getColour())),
0, 1);
if (setting.hasThreshold())
{
else
{
featureColours.put(setting.getType(), new FeatureColour(
- new Color(setting.getColour())));
+ new Colour(new Color(setting.getColour()))));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
}
}
af.setMenusFromViewport(af.viewport);
-
+ af.setTitle(view.getTitle());
// TODO: we don't need to do this if the viewport is aready visible.
/*
* Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
}
private ColourSchemeI constructAnnotationColour(
- AnnotationColours viewAnnColour, AlignFrame af, Alignment al,
+ AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
JalviewModelSequence jms, boolean checkGroupAnnColour)
{
boolean propagateAnnColour = false;
return cs;
}
- private void reorderAutoannotation(AlignFrame af, Alignment al,
+ private void reorderAutoannotation(AlignFrame af, AlignmentI al,
List<JvAnnotRow> autoAlan)
{
// copy over visualization settings for autocalculated annotation in the
}
}
- private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
+ private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
boolean ignoreUnrefed)
{
- jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
+ jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet
+ .getDatasetId());
Vector dseqs = null;
if (ds == null)
{
for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
{
Sequence vamsasSeq = vamsasSet.getSequence(i);
- ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
}
// create a new dataset
if (ds == null)
* dataset alignment
* @param dseqs
* vector to add new dataset sequence to
+ * @param ignoreUnrefed
+ * - when true, don't create new sequences from vamsasSeq if it's id
+ * doesn't already have an asssociated Jalview sequence.
+ * @param vseqpos
+ * - used to reorder the sequence in the alignment according to the
+ * vamsasSeq array ordering, to preserve ordering of dataset
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
- AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
+ AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
SequenceI sq = seqRefIds.get(vamsasSeq.getId());
+ boolean reorder = false;
SequenceI dsq = null;
if (sq != null && sq.getDatasetSequence() != null)
{
dsq = sq.getDatasetSequence();
}
+ else
+ {
+ reorder = true;
+ }
if (sq == null && ignoreUnrefed)
{
return;
// + (post ? "appended" : ""));
}
}
+ else
+ {
+ // sequence refs are identical. We may need to update the existing dataset
+ // alignment with this one, though.
+ if (ds != null && dseqs == null)
+ {
+ int opos = ds.findIndex(dsq);
+ SequenceI tseq = null;
+ if (opos != -1 && vseqpos != opos)
+ {
+ // remove from old position
+ ds.deleteSequence(dsq);
+ }
+ if (vseqpos < ds.getHeight())
+ {
+ if (vseqpos != opos)
+ {
+ // save sequence at destination position
+ tseq = ds.getSequenceAt(vseqpos);
+ ds.replaceSequenceAt(vseqpos, dsq);
+ ds.addSequence(tseq);
+ }
+ }
+ else
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ }
}
/*
* TODO use AlignmentI here and in related methods - needs
* AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
*/
- Hashtable<String, Alignment> datasetIds = null;
+ Hashtable<String, AlignmentI> datasetIds = null;
- IdentityHashMap<Alignment, String> dataset2Ids = null;
+ IdentityHashMap<AlignmentI, String> dataset2Ids = null;
- private Alignment getDatasetFor(String datasetId)
+ private AlignmentI getDatasetFor(String datasetId)
{
if (datasetIds == null)
{
- datasetIds = new Hashtable<String, Alignment>();
+ datasetIds = new Hashtable<String, AlignmentI>();
return null;
}
if (datasetIds.containsKey(datasetId))
return null;
}
- private void addDatasetRef(String datasetId, Alignment dataset)
+ private void addDatasetRef(String datasetId, AlignmentI dataset)
{
if (datasetIds == null)
{
- datasetIds = new Hashtable<String, Alignment>();
+ datasetIds = new Hashtable<String, AlignmentI>();
}
datasetIds.put(datasetId, dataset);
}
* @param dataset
* @return
*/
- private String getDatasetIdRef(Alignment dataset)
+ private String getDatasetIdRef(AlignmentI dataset)
{
if (dataset.getDataset() != null)
{
// make a new datasetId and record it
if (dataset2Ids == null)
{
- dataset2Ids = new IdentityHashMap<Alignment, String>();
+ dataset2Ids = new IdentityHashMap<AlignmentI, String>();
}
else
{
}
else
{
- frefedSequence.add(new Object[] { dsfor, jmap });
+ frefedSequence.add(newMappingRef(dsfor, jmap));
}
}
else
djs.setEnd(jmap.getMap().getToHighest());
djs.setVamsasId(uniqueSetSuffix + sqid);
jmap.setTo(djs);
+ incompleteSeqs.put(sqid, djs);
seqRefIds.put(sqid, djs);
}
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+ import jalview.renderer.ScaleRenderer;
+ import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.util.ColorUtils;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
updateViewport();
- int scalestartx = startx - (startx % 10) + 10;
-
- g.setColor(Color.black);
- // NORTH SCALE
- for (int i = scalestartx; i < endx; i += 10)
+ for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+ endx))
{
- int value = i;
- if (av.hasHiddenColumns())
+ int mpos = mark.column; // (i - startx - 1)
+ if (mpos < 0)
{
- value = av.getColumnSelection().adjustForHiddenColumns(value);
+ continue;
}
+ String mstring = mark.text;
- g.drawString(String.valueOf(value), (i - startx - 1) * charWidth,
- ypos - (charHeight / 2));
-
- g.drawLine(((i - startx - 1) * charWidth) + (charWidth / 2),
- (ypos + 2) - (charHeight / 2), ((i - startx - 1) * charWidth)
- + (charWidth / 2), ypos - 2);
+ if (mark.major)
+ {
+ if (mstring != null)
+ {
+ g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
+ }
+ g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2)
+ - (charHeight / 2), (mpos * charWidth) + (charWidth / 2),
+ ypos - 2);
+ }
}
}
else
{
g.setStroke(new BasicStroke());
- g.setColor(group.getOutlineColour());
+ g.setColor(ColorUtils.getColor(group.getOutlineColour()));
}
}
}
*/
package jalview.gui;
+import jalview.api.ColorI;
import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.schemes.Colour;
import jalview.schemes.ColourSchemeI;
+import jalview.util.ColorUtils;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
- /**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
final static int CHAR_TO_UPPER = 'A' - 'a';
}
@Override
- public Color getResidueBoxColour(SequenceI seq, int i)
+ public ColorI getResidueBoxColour(SequenceI seq, int i)
{
+ // rate limiting step when rendering overview for lots of groups
allGroups = av.getAlignment().findAllGroups(seq);
if (inCurrentSequenceGroup(i))
getBoxColour(av.getGlobalColourScheme(), seq, i);
}
- return resBoxColour;
+ return new Colour(resBoxColour);
}
/**
* @return
*/
@Override
- public Color getResidueColour(final SequenceI seq, int position,
+ public ColorI getResidueColour(final SequenceI seq, int position,
FeatureRenderer fr)
{
// TODO replace 8 or so code duplications with calls to this method
// (refactored as needed)
- Color col = getResidueBoxColour(seq, position);
+ ColorI col = getResidueBoxColour(seq, position);
if (fr != null)
{
{
end = seq.getLength() - 1;
}
- graphics.setColor(av.getTextColour());
+ graphics.setColor(ColorUtils.getColor(av.getTextColour()));
if (monospacedFont && av.getShowText() && allGroups.length == 0
&& !av.getColourText() && av.getThresholdTextColour() == 0)
for (int i = start; i <= end; i++)
{
- graphics.setColor(av.getTextColour());
+ graphics.setColor(ColorUtils.getColor(av.getTextColour()));
getboxColour = false;
s = seq.getCharAt(i);
if (resBoxColour.getRed() + resBoxColour.getBlue()
+ resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
{
- graphics.setColor(currentSequenceGroup.textColour2);
+ graphics.setColor(ColorUtils.getColor(currentSequenceGroup.textColour2));
}
}
}
else
{
- graphics.setColor(currentSequenceGroup.textColour);
+ graphics.setColor(ColorUtils.getColor(currentSequenceGroup.textColour));
}
if (!isarep && !isgrep
&& currentSequenceGroup.getShowNonconserved()) // todo
if (resBoxColour.getRed() + resBoxColour.getBlue()
+ resBoxColour.getGreen() < av.getThresholdTextColour())
{
- graphics.setColor(av.getTextColour2());
+ graphics.setColor(ColorUtils.getColor(av.getTextColour2()));
}
}
if (!isarep && av.getShowUnconserved())
{
- s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
+ s = getDisplayChar(srep, i, s, '.', null);
}
{
// TODO - use currentSequenceGroup rather than alignment
// currentSequenceGroup.getConsensus()
- char conschar = (usesrep) ? (currentGroup == null ? av.getAlignment()
+ char conschar = (usesrep) ? (currentGroup == null
+ || position < currentGroup.getStartRes()
+ || position > currentGroup.getEndRes() ? av.getAlignment()
.getSeqrep().getCharAt(position)
: (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
.getCharAt(position) : av.getAlignment().getSeqrep()
.getCharAt(position)))
- : (currentGroup != null && currentGroup.getConsensus() != null) ? currentGroup
+ : (currentGroup != null && currentGroup.getConsensus() != null
+ && position >= currentGroup.getStartRes()
+ && position <= currentGroup.getEndRes() && currentGroup
+ .getConsensus().annotations.length > position) ? currentGroup
.getConsensus().annotations[position].displayCharacter
.charAt(0)
: av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
package jalview.gui;
import jalview.datamodel.SequenceGroup;
+import jalview.schemes.Colour;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
final JPanel col2 = new JPanel();
col2.setPreferredSize(new Dimension(40, 20));
col2.setBorder(BorderFactory.createEtchedBorder());
- col2.setToolTipText(MessageManager.getString("label.ligth_colour"));
+ col2.setToolTipText(MessageManager.getString("label.light_colour"));
col2.setBackground(new Color(original2));
final JPanel bigpanel = new JPanel(new BorderLayout());
JPanel panel = new JPanel();
new JLabel(
"<html>"
+ MessageManager
- .getString("label.select_dark_light_set_thereshold")
+ .getString("label.select_dark_light_set_threshold")
+ "</html>"), BorderLayout.NORTH);
panel.add(col1);
panel.add(slider);
ap,
bigpanel,
MessageManager
- .getString("label.adjunst_foreground_text_colour_thereshold"),
+ .getString("label.adjunst_foreground_text_colour_threshold"),
JOptionPane.OK_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE, null, null, null);
{
if (sg == null)
{
- ap.av.setTextColour(new Color(original1));
- ap.av.setTextColour2(new Color(original2));
+ ap.av.setTextColour(new Colour(original1));
+ ap.av.setTextColour2(new Colour(original2));
ap.av.setThresholdTextColour(originalThreshold);
}
else
{
- sg.textColour = new Color(original1);
- sg.textColour2 = new Color(original2);
+ sg.textColour = new Colour(original1);
+ sg.textColour2 = new Colour(original2);
sg.thresholdTextColour = originalThreshold;
}
}
{
if (sg == null)
{
- ap.av.setTextColour(col);
+ ap.av.setTextColour(new Colour(col));
if (ap.av.getColourAppliesToAllGroups())
{
setGroupTextColour();
}
else
{
- sg.textColour = col;
+ sg.textColour = new Colour(col);
}
ap.paintAlignment(true);
{
if (sg == null)
{
- ap.av.setTextColour2(col);
+ ap.av.setTextColour2(new Colour(col));
if (ap.av.getColourAppliesToAllGroups())
{
setGroupTextColour();
}
else
{
- sg.textColour2 = col;
+ sg.textColour2 = new Colour(col);
}
ap.paintAlignment(true);
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
+import jalview.schemes.Colour;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.structure.SelectionSource;
+import jalview.util.ColorUtils;
import jalview.util.Format;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import javax.swing.JColorChooser;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+ import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
/**
tree.findHeight(tree.getTopNode());
// Now have to calculate longest name based on the leaves
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+ Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
boolean has_placeholders = false;
longestName = "";
for (int i = 0; i < leaves.size(); i++)
{
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+ SequenceNode lf = leaves.elementAt(i);
if (lf.isPlaceholder())
{
}
else
{
- g.setColor(av.getSequenceColour(seq).darker());
+ g.setColor(ColorUtils.getColor(av.getSequenceColour(seq))
+ .darker());
}
}
else
for (int a = 0; a < aps.length; a++)
{
final SequenceI seq = (SequenceI) node.element();
- aps[a].av.setSequenceColour(seq, c);
+ aps[a].av.setSequenceColour(seq, new Colour(c));
}
}
}
}
/**
- * DOCUMENT ME!
+ * Empty method to satisfy the MouseListener interface
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseReleased(MouseEvent e)
{
+ /*
+ * isPopupTrigger is set on mouseReleased on Windows
+ */
+ if (e.isPopupTrigger())
+ {
+ chooseSubtreeColour();
+ e.consume(); // prevent mouseClicked happening
+ }
}
/**
- * DOCUMENT ME!
+ * Empty method to satisfy the MouseListener interface
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseEntered(MouseEvent e)
}
/**
- * DOCUMENT ME!
+ * Empty method to satisfy the MouseListener interface
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseExited(MouseEvent e)
}
/**
- * DOCUMENT ME!
+ * Handles a mouse click on a tree node (clicks elsewhere are handled in
+ * mousePressed). Click selects the sub-tree, double-click swaps leaf nodes
+ * order, right-click opens a dialogue to choose colour for the sub-tree.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseClicked(MouseEvent evt)
{
- if (highlightNode != null)
+ if (highlightNode == null)
{
- if (evt.isPopupTrigger())
- {
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_subtree_colour"),
- highlightNode.color);
- if (col != null)
- {
- setColor(highlightNode, col);
- }
- }
- else if (evt.getClickCount() > 1)
+ return;
+ }
+
+ if (evt.getClickCount() > 1)
+ {
+ tree.swapNodes(highlightNode);
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ }
+ else
+ {
+ Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
+
+ for (int i = 0; i < leaves.size(); i++)
{
- tree.swapNodes(highlightNode);
- tree.reCount(tree.getTopNode());
- tree.findHeight(tree.getTopNode());
+ SequenceI seq = (SequenceI) leaves.elementAt(i)
+ .element();
+ treeSelectionChanged(seq);
}
- else
- {
- Vector leaves = new Vector();
- tree.findLeaves(highlightNode, leaves);
+ av.sendSelection();
+ }
- for (int i = 0; i < leaves.size(); i++)
- {
- SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
- .element();
- treeSelectionChanged(seq);
- }
- av.sendSelection();
- }
+ PaintRefresher.Refresh(tp, av.getSequenceSetId());
+ repaint();
+ }
- PaintRefresher.Refresh(tp, av.getSequenceSetId());
+ /**
+ * Offer the user the option to choose a colour for the highlighted node and
+ * its children; this colour is also applied to the corresponding sequence ids
+ * in the alignment
+ */
+ void chooseSubtreeColour()
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_subtree_colour"),
+ highlightNode.color);
+ if (col != null)
+ {
+ setColor(highlightNode, col);
+ PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
repaint();
}
}
}
/**
- * DOCUMENT ME!
+ * Handles a mouse press on a sequence name or the tree background canvas
+ * (click on a node is handled in mouseClicked). The action is to create
+ * groups by partitioning the tree at the mouse position. Colours for the
+ * groups (and sequence names) are generated randomly.
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mousePressed(MouseEvent e)
{
av.setCurrentTree(tree);
+ /*
+ * isPopupTrigger is set for mousePressed (Mac)
+ * or mouseReleased (Windows)
+ */
+ if (e.isPopupTrigger())
+ {
+ if (highlightNode != null)
+ {
+ chooseSubtreeColour();
+ }
+ return;
+ }
+
+ /*
+ * defer right-click handling on Windows to
+ * mouseClicked; note isRightMouseButton
+ * also matches Cmd-click on Mac which should do
+ * nothing here
+ */
+ if (SwingUtilities.isRightMouseButton(e))
+ {
+ return;
+ }
+
int x = e.getX();
int y = e.getY();
{
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
- setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
+ setColor(tree.getGroups().elementAt(i), col.brighter());
- Vector l = tree.findLeaves(
- (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+ Vector<SequenceNode> l = tree.findLeaves(tree
+ .getGroups().elementAt(i));
- Vector sequences = new Vector();
+ Vector<SequenceI> sequences = new Vector<SequenceI>();
for (int j = 0; j < l.size(); j++)
{
- SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
+ SequenceI s1 = (SequenceI) l.elementAt(j)
.element();
if (!sequences.contains(s1))
.getCodingComplement();
if (codingComplement != null)
{
- if (codingComplement != null)
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
+ codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
{
- SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
- av, codingComplement);
- if (mappedGroup.getSequences().size() > 0)
+ codingComplement.getAlignment().addGroup(mappedGroup);
+ for (SequenceI seq : mappedGroup.getSequences())
{
- codingComplement.getAlignment().addGroup(mappedGroup);
- for (SequenceI seq : mappedGroup.getSequences())
- {
- codingComplement.setSequenceColour(seq,
- new Colour(col.brighter()));
- }
- codingComplement.setSequenceColour(seq, col.brighter());
++ codingComplement.setSequenceColour(seq,
++ new Colour(col.brighter()));
}
}
}
{
((AlignViewport) codingComplement).getAlignPanel()
.updateAnnotation();
-
}
-
}
-
}
/**
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.schemes.Colour;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ResidueProperties;
}
else if (key.equalsIgnoreCase("textCol1"))
{
- sg.textColour = new UserColourScheme(value).findColour('A');
+ sg.textColour = new Colour(
+ new UserColourScheme(value).findColour('A'));
}
else if (key.equalsIgnoreCase("textCol2"))
{
- sg.textColour2 = new UserColourScheme(value).findColour('A');
+ sg.textColour2 = new Colour(
+ new UserColourScheme(value).findColour('A'));
}
else if (key.equalsIgnoreCase("textColThreshold"))
{
*/
public String printCSVAnnotations(AlignmentAnnotation[] annotations)
{
+ if (annotations == null)
+ {
+ return "";
+ }
StringBuffer sp = new StringBuffer();
for (int i = 0; i < annotations.length; i++)
{
import jalview.io.gff.GffHelperI;
import jalview.schemes.FeatureColour;
import jalview.schemes.UserColourScheme;
- import jalview.util.Format;
import jalview.util.MapList;
import jalview.util.ParseHtmlBodyAndLinks;
import jalview.util.StringUtils;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.StringTokenizer;
/**
* Parses and writes features files, which may be in Jalview, GFF2 or GFF3
else if (ft.equalsIgnoreCase("endgroup"))
{
// We should check whether this is the current group,
- // but at present theres no way of showing more than 1 group
+ // but at present there's no way of showing more than 1 group
featureGroup = null;
}
else
{
- parseFeatureColour(line, ft, gffColumns, colours);
+ String colscheme = gffColumns[1];
+ FeatureColourI colour = FeatureColour
+ .parseJalviewFeatureColour(colscheme);
+ if (colour != null)
+ {
+ colours.put(ft, colour);
+ }
}
continue;
}
}
/**
+ * Process a feature type colour specification
+ *
+ * @param line
+ * the current input line (for error messages only)
+ * @param featureType
+ * the first token on the line
+ * @param gffColumns
+ * holds tokens on the line
+ * @param colours
+ * map to which to add derived colour specification
+ */
+ protected void parseFeatureColour(String line, String featureType,
+ String[] gffColumns, Map<String, FeatureColourI> colours)
+ {
+ FeatureColourI colour = null;
+ String colscheme = gffColumns[1];
+ if (colscheme.indexOf("|") > -1
+ || colscheme.trim().equalsIgnoreCase("label"))
+ {
+ colour = parseGraduatedColourScheme(line, colscheme);
+ }
+ else
+ {
+ UserColourScheme ucs = new UserColourScheme(colscheme);
+ colour = new FeatureColour(ucs.findColour('A'));
+ }
+ if (colour != null)
+ {
+ colours.put(featureType, colour);
+ }
+ }
+
+ /**
+ * Parse a Jalview graduated colour descriptor
+ *
+ * @param line
+ * @param colourDescriptor
+ * @return
+ */
+ protected FeatureColourI parseGraduatedColourScheme(String line,
+ String colourDescriptor)
+ {
+ // Parse '|' separated graduated colourscheme fields:
+ // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]
+ // can either provide 'label' only, first is optional, next two
+ // colors are required (but may be
+ // left blank), next is optional, nxt two min/max are required.
+ // first is either 'label'
+ // first/second and third are both hexadecimal or word equivalent
+ // colour.
+ // next two are values parsed as floats.
+ // fifth is either 'above','below', or 'none'.
+ // sixth is a float value and only required when fifth is either
+ // 'above' or 'below'.
+ StringTokenizer gcol = new StringTokenizer(colourDescriptor, "|", true);
+ // set defaults
+ float min = Float.MIN_VALUE, max = Float.MAX_VALUE;
+ boolean labelCol = false;
+ // Parse spec line
+ String mincol = gcol.nextToken();
+ if (mincol == "|")
+ {
+ System.err
+ .println("Expected either 'label' or a colour specification in the line: "
+ + line);
+ return null;
+ }
+ String maxcol = null;
+ if (mincol.toLowerCase().indexOf("label") == 0)
+ {
+ labelCol = true;
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip '|'
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ }
+ String abso = null, minval, maxval;
+ if (mincol != null)
+ {
+ // at least four more tokens
+ if (mincol.equals("|"))
+ {
+ mincol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ // continue parsing rest of line
+ maxcol = gcol.nextToken();
+ if (maxcol.equals("|"))
+ {
+ maxcol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ abso = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ if (abso.toLowerCase().indexOf("abso") != 0)
+ {
+ minval = abso;
+ abso = null;
+ }
+ else
+ {
+ minval = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ }
+ maxval = gcol.nextToken();
+ if (gcol.hasMoreTokens())
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ try
+ {
+ if (minval.length() > 0)
+ {
+ min = Float.valueOf(minval);
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the minimum value for graduated colour for type ("
+ + colourDescriptor
+ + ") - did you misspell 'auto' for the optional automatic colour switch ?");
+ e.printStackTrace();
+ }
+ try
+ {
+ if (maxval.length() > 0)
+ {
+ max = Float.valueOf(maxval);
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the maximum value for graduated colour for type ("
+ + colourDescriptor + ")");
+ e.printStackTrace();
+ }
+ }
+ else
+ {
+ // add in some dummy min/max colours for the label-only
+ // colourscheme.
+ mincol = "FFFFFF";
+ maxcol = "000000";
+ }
+
+ FeatureColourI colour = null;
+ try
+ {
+ colour = new FeatureColour(
+ new UserColourScheme(mincol).findColour('A'),
+ new UserColourScheme(maxcol).findColour('A'), min, max);
+ } catch (Exception e)
+ {
+ System.err.println("Couldn't parse the graduated colour scheme ("
+ + colourDescriptor + ")");
+ e.printStackTrace();
+ }
+ if (colour != null)
+ {
+ colour.setColourByLabel(labelCol);
+ colour.setAutoScaled(abso == null);
+ // add in any additional parameters
+ String ttype = null, tval = null;
+ boolean hasThreshold = false;
+ if (gcol.hasMoreTokens())
+ {
+ // threshold type and possibly a threshold value
+ ttype = gcol.nextToken();
+ if (ttype.toLowerCase().startsWith("below"))
+ {
+ colour.setBelowThreshold(true);
+ hasThreshold = true;
+ }
+ else if (ttype.toLowerCase().startsWith("above"))
+ {
+ colour.setAboveThreshold(true);
+ hasThreshold = true;
+ }
+ else
+ {
+ if (!ttype.toLowerCase().startsWith("no"))
+ {
+ System.err.println("Ignoring unrecognised threshold type : "
+ + ttype);
+ }
+ }
+ }
+ if (hasThreshold)
+ {
+ try
+ {
+ gcol.nextToken();
+ tval = gcol.nextToken();
+ colour.setThreshold(new Float(tval).floatValue());
+ } catch (Exception e)
+ {
+ System.err.println("Couldn't parse threshold value as a float: ("
+ + tval + ")");
+ e.printStackTrace();
+ }
+ }
+ // parse the thresh-is-min token ?
+ if (gcol.hasMoreTokens())
+ {
+ System.err
+ .println("Ignoring additional tokens in parameters in graduated colour specification\n");
+ while (gcol.hasMoreTokens())
+ {
+ System.err.println("|" + gcol.nextToken());
+ }
+ System.err.println("\n");
+ }
+ }
+ return colour;
+ }
+
+ /**
* clear any temporary handles used to speed up ID matching
*/
protected void resetMatcher()
*
* @param sequences
* source of features
- * @param visible
+ * @param featureColours
* hash of Colours for each feature type
* @param visOnly
* when true only feature types in 'visible' will be output
* @return features file contents
*/
public String printJalviewFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible, boolean visOnly,
+ Map<String, FeatureColourI> featureColours, boolean visOnly,
boolean nonpos)
{
StringBuilder out = new StringBuilder(256);
boolean featuresGen = false;
- if (visOnly && !nonpos && (visible == null || visible.size() < 1))
+ if (visOnly && !nonpos
+ && (featureColours == null || featureColours.size() < 1))
{
// no point continuing.
return "No Features Visible";
}
- if (visible != null && visOnly)
+ if (featureColours != null && visOnly)
{
// write feature colours only if we're given them and we are generating
// viewed features
// TODO: decide if feature links should also be written here ?
- Iterator<String> en = visible.keySet().iterator();
+ Iterator<String> en = featureColours.keySet().iterator();
- String featureType, color;
while (en.hasNext())
{
- featureType = en.next();
- FeatureColourI fc = featureColours.get(featureType);
- if (fc.isSimpleColour())
- {
- color = Format.getHexString(fc.getColour());
- }
- else
- {
- color = (fc.isColourByLabel() ? "label|" : "")
- + Format.getHexString(fc.getMinColour()) + "|"
- + Format.getHexString(fc.getMaxColour())
- + (fc.isAutoScaled() ? "|" : "|abso|") + fc.getMin() + "|"
- + fc.getMax() + "|";
- if (fc.isBelowThreshold())
- {
- color += "below";
- }
- else if (fc.isAboveThreshold())
- {
- color += "above";
- }
- // add the value
- color += "|" + fc.getThreshold();
- }
- // else
- // {
- // color += "none";
- // }
- // else
- // {
- // // legacy support for integer objects containing colour triplet
- // values
- // color = Format.getHexString(new Color(Integer
- // .parseInt(fc.toString())));
- // }
- out.append(featureType);
- out.append(TAB);
- out.append(color);
- out.append(newline);
- String featureType = en.next().toString();
- FeatureColourI colour = visible.get(featureType);
++ String featureType = en.next();
++ FeatureColourI colour = featureColours.get(featureType);
+ out.append(colour.toJalviewFormat(featureType)).append(newline);
}
}
+
// Work out which groups are both present and visible
List<String> groups = new ArrayList<String>();
int groupIndex = 0;
{
isnonpos = features[j].begin == 0 && features[j].end == 0;
if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
+ || (!isnonpos && visOnly && !featureColours
.containsKey(features[j].type)))
{
continue;
features = sequences[i].getSequenceFeatures();
if (features != null)
{
- for (int j = 0; j < features.length; j++)
+ for (SequenceFeature sequenceFeature : features)
{
- isnonpos = features[j].begin == 0 && features[j].end == 0;
+ isnonpos = sequenceFeature.begin == 0 && sequenceFeature.end == 0;
if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
+ || (!isnonpos && visOnly && !featureColours
- .containsKey(features[j].type)))
+ .containsKey(sequenceFeature.type)))
{
// skip if feature is nonpos and we ignore them or if we only
// output visible and it isn't non-pos and it's not visible
}
if (group != null
- && (features[j].featureGroup == null || !features[j].featureGroup
+ && (sequenceFeature.featureGroup == null || !sequenceFeature.featureGroup
.equals(group)))
{
continue;
}
- if (group == null && features[j].featureGroup != null)
+ if (group == null && sequenceFeature.featureGroup != null)
{
continue;
}
// we have features to output
featuresGen = true;
- if (features[j].description == null
- || features[j].description.equals(""))
+ if (sequenceFeature.description == null
+ || sequenceFeature.description.equals(""))
{
- out.append(features[j].type).append(TAB);
+ out.append(sequenceFeature.type).append(TAB);
}
else
{
- if (features[j].links != null
- && features[j].getDescription().indexOf("<html>") == -1)
+ if (sequenceFeature.links != null
+ && sequenceFeature.getDescription().indexOf("<html>") == -1)
{
out.append("<html>");
}
- out.append(features[j].description + " ");
- if (features[j].links != null)
+ out.append(sequenceFeature.description);
+ if (sequenceFeature.links != null)
{
- for (int l = 0; l < features[j].links.size(); l++)
+ for (int l = 0; l < sequenceFeature.links.size(); l++)
{
- String label = features[j].links.elementAt(l).toString();
+ String label = sequenceFeature.links.elementAt(l);
String href = label.substring(label.indexOf("|") + 1);
label = label.substring(0, label.indexOf("|"));
- if (features[j].description.indexOf(href) == -1)
+ if (sequenceFeature.description.indexOf(href) == -1)
{
- out.append("<a href=\"" + href + "\">" + label + "</a>");
+ out.append(" <a href=\"" + href + "\">" + label
+ + "</a>");
}
}
- if (features[j].getDescription().indexOf("</html>") == -1)
+ if (sequenceFeature.getDescription().indexOf("</html>") == -1)
{
out.append("</html>");
}
}
out.append(sequences[i].getName());
out.append("\t-1\t");
- out.append(features[j].begin);
+ out.append(sequenceFeature.begin);
out.append(TAB);
- out.append(features[j].end);
+ out.append(sequenceFeature.end);
out.append(TAB);
- out.append(features[j].type);
- if (!Float.isNaN(features[j].score))
+ out.append(sequenceFeature.type);
+ if (!Float.isNaN(sequenceFeature.score))
{
out.append(TAB);
- out.append(features[j].score);
+ out.append(sequenceFeature.score);
}
out.append(newline);
}
*
* @param sequences
* the sequences whose features are to be output
- * @param visible
+ * @param featureColours
* a map whose keys are the type names of visible features
* @param outputVisibleOnly
* @param includeNonPositionalFeatures
* @return
*/
public String printGffFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible, boolean outputVisibleOnly,
+ Map<String, FeatureColourI> featureColours,
+ boolean outputVisibleOnly,
boolean includeNonPositionalFeatures)
{
StringBuilder out = new StringBuilder(256);
- out.append(String.format("%s %d\n", GFF_VERSION, gffVersion));
+ int version = gffVersion == 0 ? 2 : gffVersion;
+ out.append(String.format("%s %d\n", GFF_VERSION, version));
String source;
boolean isnonpos;
for (SequenceI seq : sequences)
// TODO why the test !isnonpos here?
// what about not visible non-positional features?
if (!isnonpos && outputVisibleOnly
- && !visible.containsKey(sf.type))
+ && !featureColours.containsKey(sf.type))
{
/*
* ignore not visible features if not wanted
import jalview.gui.IProgressIndicator;
import jalview.gui.OOMWarning;
import jalview.math.AlignmentDimension;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import java.awt.Color;
AlignmentPanel ap;
+ private IProgressIndicator pIndicator;
+
+ private long pSessionId;
+
+ private boolean headless;
+
+
public HtmlSvgOutput(File file, AlignmentPanel ap)
{
this.av = ap.av;
public void generateHtmlSvgOutput(File file)
{
- IProgressIndicator pIndicator = ap.alignFrame;
- long pSessionId = System.currentTimeMillis();
+ pIndicator = ap.alignFrame;
+ pSessionId = System.currentTimeMillis();
try
{
- boolean headless = (System.getProperty("java.awt.headless") != null && System
+ headless = (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true"));
if (file == null)
{
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "status.waiting_for_user_to_select_output_file", "HTML"),
- pSessionId);
- }
+ setProgressMessage(MessageManager.formatMessage(
+ "status.waiting_for_user_to_select_output_file", "HTML"));
JalviewFileChooser chooser = getHTMLChooser();
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(ap.alignFrame.getTitle());
jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
file = chooser.getSelectedFile();
+ ap.alignFrame.repaint();
}
else
{
-
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "status.cancelled_image_export_operation", "HTML"),
- pSessionId);
- }
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "HTML"));
return;
}
}
-
- AlignmentDimension aDimension = ap.getAlignmentDimension();
- SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
- aDimension.getHeight());
- SVGGraphics2D g2 = new SVGGraphics2D(aDimension.getWidth(),
- aDimension.getHeight());
-
- String renderStyle = jalview.bin.Cache.getDefault("HTML_RENDERING",
- "Prompt each time");
-
- // If we need to prompt, and if the GUI is visible then
- // Prompt for rendering style
- if (renderStyle.equalsIgnoreCase("Prompt each time")
- && !(System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
+ } catch (Exception e)
+ {
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "info.error_creating_file", "HTML"), pSessionId);
+ e.printStackTrace();
+ return;
+ }
+ final File fileX = file;
+ new Thread()
+ {
+ @Override
+ public void run()
{
- HTMLOptions svgOption = new HTMLOptions();
- renderStyle = svgOption.getValue();
-
- if (renderStyle == null || svgOption.cancelled)
+ try
{
- return;
- }
- }
+ setProgressMessage(null);
+ setProgressMessage(MessageManager
+ .formatMessage(
+ "status.exporting_alignment_as_x_file", "HTML"));
+ AlignmentDimension aDimension = ap.getAlignmentDimension();
+ SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
+ aDimension.getHeight());
+ SVGGraphics2D g2 = new SVGGraphics2D(aDimension.getWidth(),
+ aDimension.getHeight());
- if (renderStyle.equalsIgnoreCase("lineart"))
- {
- g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
- SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
- g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
- SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
- }
- printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, g1,
- g2);
-
- String titleSvgData = g1.getSVGDocument();
- String alignSvgData = g2.getSVGDocument();
- String jsonData = null;
- boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache
- .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
- if (isEmbbedBioJSON)
- {
- AlignExportSettingI exportSettings = new AlignExportSettingI()
- {
- @Override
- public boolean isExportHiddenSequences()
- {
- return true;
- }
+ String renderStyle = jalview.bin.Cache.getDefault(
+ "HTML_RENDERING", "Prompt each time");
- @Override
- public boolean isExportHiddenColumns()
+ // If we need to prompt, and if the GUI is visible then
+ // Prompt for rendering style
+ if (renderStyle.equalsIgnoreCase("Prompt each time")
+ && !(System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true")))
{
- return true;
- }
+ HTMLOptions svgOption = new HTMLOptions();
+ renderStyle = svgOption.getValue();
- @Override
- public boolean isExportAnnotations()
- {
- return true;
+ if (renderStyle == null || svgOption.cancelled)
+ {
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "HTML"));
+ return;
+ }
}
- @Override
- public boolean isExportFeatures()
+ if (renderStyle.equalsIgnoreCase("Lineart"))
{
- return true;
+ g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+ SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
+ g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+ SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
}
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ g1, g2);
- @Override
- public boolean isExportGroups()
+ String titleSvgData = g1.getSVGDocument();
+ String alignSvgData = g2.getSVGDocument();
+ String jsonData = null;
+ boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache
+ .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
+ if (isEmbbedBioJSON)
{
- return true;
- }
+ AlignExportSettingI exportSettings = new AlignExportSettingI()
+ {
+ @Override
+ public boolean isExportHiddenSequences()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportAnnotations()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isExportFeatures()
+ {
+ return true;
+ }
- @Override
- public boolean isCancelled()
+ @Override
+ public boolean isExportGroups()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isCancelled()
+ {
+ return false;
+ }
+
+ };
+ AlignmentExportData exportData = jalview.gui.AlignFrame
+ .getAlignmentForExport(JSONFile.FILE_DESC, av,
+ exportSettings);
+ jsonData = new FormatAdapter(ap, exportData.getSettings())
+ .formatSequences(JSONFile.FILE_DESC,
+ exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ av.getColumnSelection());
+ }
+ String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
+ FileOutputStream out = new FileOutputStream(fileX);
+ out.write(htmlData.getBytes());
+ out.flush();
+ out.close();
+ if (!(System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true")))
{
- return false;
+ jalview.util.BrowserLauncher.openURL("file:///" + fileX);
}
-
- };
- AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(JSONFile.FILE_DESC, av,
- exportSettings);
- jsonData = new FormatAdapter(ap, exportData.getSettings())
- .formatSequences(JSONFile.FILE_DESC,
- exportData.getAlignment(),
- exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- av.getColumnSelection());
- }
- String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
- FileOutputStream out = new FileOutputStream(file);
- out.write(htmlData.getBytes());
- out.flush();
- out.close();
- if (!(System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
- {
- jalview.util.BrowserLauncher.openURL("file:///" + file);
- }
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "status.export_complete", "HTML"), pSessionId);
+ } catch (OutOfMemoryError err)
+ {
+ System.out.println("########################\n"
+ + "OUT OF MEMORY " + fileX + "\n"
+ + "########################");
+ new OOMWarning("Creating Image for " + fileX, err);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "info.error_creating_file", "HTML"), pSessionId);
+ }
+ setProgressMessage(MessageManager.formatMessage(
+ "status.export_complete", "HTML"));
}
- } catch (OutOfMemoryError err)
+ }.start();
+
+ }
+
+ private void setProgressMessage(String message)
+ {
+ if (pIndicator != null && !headless)
{
- System.out.println("########################\n" + "OUT OF MEMORY "
- + file + "\n" + "########################");
- new OOMWarning("Creating Image for " + file, err);
- } catch (Exception e)
+ pIndicator.setProgressBar(message, pSessionId);
+ }
+ else
{
- e.printStackTrace();
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "info.error_creating_file", "HTML"), pSessionId);
+ System.out.println(message);
}
}
}
else
{
- currentColor = av.getSequenceColour(seq);
+ currentColor = ColorUtils.getColor(av.getSequenceColour(seq));
currentTextColor = Color.black;
}
pg[0].setColor(currentColor);
import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
import jalview.json.binding.biojson.v1.SequenceGrpPojo;
import jalview.json.binding.biojson.v1.SequencePojo;
+import jalview.schemes.Colour;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
String.valueOf(seq.hashCode()));
String featureColour = (fr == null) ? null : jalview.util.Format
- .getHexString(fr.findFeatureColour(Color.white, seq,
+ .getHexString(fr.findFeatureColour(Colour.white, seq,
seq.findIndex(sf.getBegin())));
jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
jsonFeature.setXend(seq.findIndex(sf.getEnd()));
@Override
public void configureForView(AlignmentViewPanel avpanel)
{
+ if (avpanel == null)
+ {
+ return;
+ }
super.configureForView(avpanel);
AlignViewportI viewport = avpanel.getAlignViewport();
AlignmentI alignment = viewport.getAlignment();
fr = avpanel.cloneFeatureRenderer();
// Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : annots)
+ if (annots != null)
{
- if (annot != null && !annot.autoCalculated)
+ for (AlignmentAnnotation annot : annots)
{
- annotations.add(annot);
+ if (annot != null && !annot.autoCalculated)
+ {
+ annotations.add(annot);
+ }
}
}
globalColourScheme = ColourSchemeProperty.getColourName(viewport
package jalview.io;
+import jalview.api.ColorI;
import jalview.api.FeatureColourI;
+import jalview.schemes.Colour;
- import jalview.schemes.FeatureColourAdapter;
+ import jalview.schemes.FeatureColour;
import jalview.schemes.FeatureSettingsAdapter;
-import java.awt.Color;
-
public class PDBFeatureSettings extends FeatureSettingsAdapter
{
{
if (type.equalsIgnoreCase(FEATURE_INSERTION))
{
- return new FeatureColourAdapter()
+ return new FeatureColour()
{
@Override
- public Color getColour()
+ public ColorI getColour()
{
- return Color.RED;
+ return Colour.red;
}
};
}
*/
package jalview.renderer.seqfeatures;
+ import jalview.api.AlignViewportI;
+import jalview.api.ColorI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.schemes.Colour;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import java.awt.AlphaComposite;
boolean av_validCharWidth, av_isShowSeqFeatureHeight;
+ private Integer currentColour;
+
+ /**
+ * Constructor given a viewport
+ *
+ * @param viewport
+ */
+ public FeatureRenderer(AlignViewportI viewport)
+ {
+ this.av = viewport;
+ }
+
protected void updateAvConfig()
{
av_charHeight = av.getCharHeight();
BufferedImage offscreenImage;
@Override
- public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
+ public ColorI findFeatureColour(ColorI initialCol, SequenceI seq, int res)
{
- return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
+ return new Colour(findFeatureColour(initialCol.getRGB(), seq, res));
+ }
+
+ public ColorI findFeatureColour(Color initialCol, SequenceI seq, int res)
+ {
+ return findFeatureColour(new Colour(initialCol), seq, res);
}
/**
int epos;
- private Integer currentColour;
-
public synchronized void drawSequence(Graphics g, final SequenceI seq,
int start, int end, int y1)
{
package jalview.schemes;
+import jalview.api.ColorI;
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
import jalview.util.Format;
{
private static final String BAR = "|";
- final private Color colour;
+ final private ColorI colour;
- final private Color minColour;
+ final private ColorI minColour;
- final private Color maxColour;
+ final private ColorI maxColour;
private boolean graduatedColour;
throw new IllegalArgumentException("Invalid colour descriptor: "
+ descriptor);
}
- return new FeatureColour(colour);
+ return new FeatureColour(new Colour(colour));
}
/*
- * autoScaled == true: colours range over actual score range; autoScaled ==
- * false ('abso'): colours range over min/max range
- * autoScaled == true: colours range over actual score range
++ * autoScaled == true: colours range over actual score range;
+ * autoScaled == false ('abso'): colours range over min/max range
*/
- boolean autoScaled = false;
+ boolean autoScaled = true;
String tok = null, minval, maxval;
if (mincol != null)
{
}
tok = gcol.nextToken();
gcol.nextToken(); // skip next '|'
- if (tok.toLowerCase().indexOf("abso") != 0)
+ if (tok.toLowerCase().startsWith("abso"))
{
- minval = tok;
- autoScaled = true;
+ minval = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ autoScaled = false;
}
else
{
- minval = gcol.nextToken();
- gcol.nextToken(); // skip next '|'
+ minval = tok;
}
maxval = gcol.nextToken();
if (gcol.hasMoreTokens())
FeatureColour featureColour;
try
{
- featureColour = new FeatureColour(
- new UserColourScheme(mincol).findColour('A'),
- new UserColourScheme(maxcol).findColour('A'), min, max);
+ featureColour = new FeatureColour(new Colour(new UserColourScheme(
+ mincol).findColour('A')), new Colour(new UserColourScheme(
+ maxcol).findColour('A')), min, max);
featureColour.setColourByLabel(labelColour);
featureColour.setAutoScaled(autoScaled);
// add in any additional parameters
*/
public FeatureColour()
{
- this((Color) null);
+ this((ColorI) null);
}
/**
*
* @param c
*/
- public FeatureColour(Color c)
+ public FeatureColour(ColorI c)
{
- minColour = Color.WHITE;
- maxColour = Color.BLACK;
+ minColour = new Colour(Color.WHITE);
+ maxColour = new Colour(Color.BLACK);
minRed = 0f;
minGreen = 0f;
minBlue = 0f;
colour = c;
}
+ public FeatureColour(Color c)
+ {
+ this(new Colour(c));
+ }
+
/**
* Constructor given a colour range and a score range
*
* @param min
* @param max
*/
- public FeatureColour(Color low, Color high, float min, float max)
+ public FeatureColour(ColorI low, ColorI high, float min, float max)
{
graduatedColour = true;
colour = null;
}
}
+ public FeatureColour(Color low, Color high, float min, float max)
+ {
+ this(new Colour(low), new Colour(high), min, max);
+ }
/**
* Copy constructor
*
*/
public FeatureColour(FeatureColour fc)
{
- graduatedColour = fc.graduatedColour;
colour = fc.colour;
minColour = fc.minColour;
maxColour = fc.maxColour;
return graduatedColour;
}
-- /**
-- * Sets the 'graduated colour' flag. If true, also sets 'colour by label' to
-- * false.
-- */
- @Override
- public void setGraduatedColour(boolean b)
- {
- graduatedColour = b;
- if (b)
- {
- setColourByLabel(false);
- }
- }
-
- void setGraduatedColour(boolean b)
- {
- graduatedColour = b;
- if (b)
- {
- setColourByLabel(false);
- }
- }
-
@Override
- public Color getColour()
+ public ColorI getColour()
{
return colour;
}
@Override
- public Color getMinColour()
+ public ColorI getMinColour()
{
return minColour;
}
@Override
- public Color getMaxColour()
+ public ColorI getMaxColour()
{
return maxColour;
}
setGraduatedColour(false);
}
}
++
++ /**
++ * Sets the 'graduated colour' flag. If true, also sets 'colour by label' to
++ * false.
++ */
++ void setGraduatedColour(boolean b)
++ {
++ graduatedColour = b;
++ if (b)
++ {
++ setColourByLabel(false);
++ }
++ }
++
@Override
public boolean isBelowThreshold()
{
* @return
*/
@Override
- public Color getColor(SequenceFeature feature)
+ public ColorI getColor(SequenceFeature feature)
{
if (isColourByLabel())
{
- return UserColourScheme
- .createColourFromName(feature.getDescription());
+ return new Colour(UserColourScheme.createColourFromName(feature
+ .getDescription()));
}
if (!isGraduatedColour())
{
scl = 1f;
}
- return new Color(minRed + scl * deltaRed, minGreen + scl * deltaGreen, minBlue + scl * deltaBlue);
+ return new Colour(new Color(minRed + scl * deltaRed, minGreen + scl
+ * deltaGreen, minBlue + scl * deltaBlue));
}
/**
{
sb.append(Format.getHexString(getMinColour())).append(BAR);
sb.append(Format.getHexString(getMaxColour())).append(BAR);
- if (isAutoScaled())
+ if (!isAutoScaled())
{
sb.append("abso").append(BAR);
}
--- /dev/null
+package jalview.schemes;
+
+import jalview.api.ColorI;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SequenceFeature;
+
+/**
+ * A convenience class with implementations of FeatureColourI methods. Override
+ * methods as required in subclasses.
+ */
+public class FeatureColourAdapter implements FeatureColourI
+{
+ @Override
+ public boolean isGraduatedColour()
+ {
+ return isColourByLabel() || isAboveThreshold() || isBelowThreshold();
+ }
+
+ @Override
+ public ColorI getColour()
+ {
+ return Colour.black;
+ }
+
+ @Override
+ public ColorI getMinColour()
+ {
+ return Colour.white;
+ }
+
+ @Override
+ public ColorI getMaxColour()
+ {
+ return Colour.black;
+ }
+
+ @Override
+ public boolean isColourByLabel()
+ {
+ return false;
+ }
+
+ @Override
+ public boolean isBelowThreshold()
+ {
+ return false;
+ }
+
+ @Override
+ public boolean isAboveThreshold()
+ {
+ return false;
+ }
+
+ @Override
+ public boolean isThresholdMinMax()
+ {
+ return false;
+ }
+
+ @Override
+ public float getThreshold()
+ {
+ return 0f;
+ }
+
+ @Override
+ public float getMax()
+ {
+ return 0;
+ }
+
+ @Override
+ public float getMin()
+ {
+ return 0;
+ }
+
+ @Override
+ public boolean hasThreshold()
+ {
+ return false;
+ }
+
+ @Override
+ public ColorI getColor(SequenceFeature feature)
+ {
+ return null;
+ }
+
+ @Override
+ public boolean isColored(SequenceFeature feature)
+ {
+ return false;
+ }
+
+ @Override
+ public void updateBounds(float min, float max)
+ {
+ }
+
+ @Override
+ public String toJalviewFormat(String featureType)
+ {
+ return null;
+ }
+
+ @Override
+ public void setThreshold(float f)
+ {
+ }
+
+ @Override
+ public boolean isAutoScaled()
+ {
+ return false;
+ }
+
+ @Override
+ public void setAutoScaled(boolean b)
+ {
+ }
+
+ @Override
+ public boolean isSimpleColour()
+ {
+ return false;
+ }
+
+ @Override
+ public void setAboveThreshold(boolean b)
+ {
+ }
+
+ @Override
+ public void setThresholdMinMax(boolean b)
+ {
+ }
+
+ @Override
+ public void setBelowThreshold(boolean b)
+ {
+ }
+
+ @Override
+ public void setColourByLabel(boolean b)
+ {
+ }
+
- @Override
- public void setGraduatedColour(boolean b)
- {
- }
-
+}
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.ColorI;
import jalview.api.FeaturesDisplayedI;
import jalview.api.ViewStyleI;
import jalview.commands.CommandI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.Colour;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
-import java.awt.Color;
import java.util.ArrayDeque;
import java.util.ArrayList;
import java.util.BitSet;
&& !al.getCodonFrames().isEmpty())
{
/*
- * fudge - check first mapping is protein-to-nucleotide
+ * fudge - check first for protein-to-nucleotide mappings
* (we don't want to do this for protein-to-protein)
*/
- AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
- // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
- MapList[] mapLists = mapping.getdnaToProt();
- // mapLists can be empty if project load has not finished resolving seqs
- if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+ boolean doConsensus = false;
+ for (AlignedCodonFrame mapping : al.getCodonFrames())
+ {
+ // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+ MapList[] mapLists = mapping.getdnaToProt();
+ // mapLists can be empty if project load has not finished resolving seqs
+ if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+ {
+ doConsensus = true;
+ break;
+ }
+ }
+ if (doConsensus)
{
if (calculator
.getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
{
updateHiddenColumns();
}
+ isColSelChanged(true);
}
/**
}
@Override
+ public boolean hasSelectedColumns()
+ {
+ ColumnSelection columnSelection = getColumnSelection();
+ return columnSelection != null && columnSelection.hasSelectedColumns();
+ }
+
+ @Override
public boolean hasHiddenColumns()
{
return colSel != null && colSel.hasHiddenColumns();
*/
public boolean isColSelChanged(boolean b)
{
- int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel
- .hashCode();
+ int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
if (hc != -1 && hc != colselhash)
{
if (b)
protected boolean showConsensus = true;
- private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+ private Map<SequenceI, ColorI> sequenceColours = new HashMap<SequenceI, ColorI>();
protected SequenceAnnotationOrder sortAnnotationsBy = null;
colSel.hideSelectedColumns();
setSelectionGroup(null);
-
+ isColSelChanged(true);
}
public void hideColumns(int start, int end)
{
colSel.hideColumns(start, end);
}
+ isColSelChanged(true);
}
public void showColumn(int col)
{
colSel.revealHiddenColumns(col);
-
+ isColSelChanged(true);
}
public void showAllHiddenColumns()
{
colSel.revealAllHiddenColumns();
+ isColSelChanged(true);
}
// common hide/show seq stuff
}
/**
+ * Hides the specified sequence, or the sequences it represents
+ *
+ * @param sequence
+ * the sequence to hide, or keep as representative
+ * @param representGroup
+ * if true, hide the current selection group except for the
+ * representative sequence
+ */
+ public void hideSequences(SequenceI sequence, boolean representGroup)
+ {
+ if (selectionGroup == null || selectionGroup.getSize() < 1)
+ {
+ hideSequence(new SequenceI[] { sequence });
+ return;
+ }
+
+ if (representGroup)
+ {
+ hideRepSequences(sequence, selectionGroup);
+ setSelectionGroup(null);
+ return;
+ }
+
+ int gsize = selectionGroup.getSize();
+ SequenceI[] hseqs = selectionGroup.getSequences().toArray(
+ new SequenceI[gsize]);
+
+ hideSequence(hseqs);
+ setSelectionGroup(null);
+ sendSelection();
+ }
+
+ /**
* Set visibility for any annotations for the given sequence.
*
* @param sequenceI
protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
boolean visible)
{
- for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+ AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+ if (anns != null)
{
- if (ann.sequenceRef == sequenceI)
+ for (AlignmentAnnotation ann : anns)
{
- ann.visible = visible;
+ if (ann.sequenceRef == sequenceI)
+ {
+ ann.visible = visible;
+ }
}
}
}
@Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
+ return getViewAsString(selectedRegionOnly, true);
+ }
+
+ @Override
+ public String[] getViewAsString(boolean selectedRegionOnly,
+ boolean exportHiddenSeqs)
+ {
String[] selection = null;
SequenceI[] seqs = null;
int i, iSize;
}
else
{
- if (hasHiddenRows())
+ if (hasHiddenRows() && exportHiddenSeqs)
{
- iSize = alignment.getHiddenSequences().getFullAlignment()
- .getHeight();
- seqs = alignment.getHiddenSequences().getFullAlignment()
- .getSequencesArray();
- end = alignment.getHiddenSequences().getFullAlignment().getWidth();
+ AlignmentI fullAlignment = alignment.getHiddenSequences()
+ .getFullAlignment();
+ iSize = fullAlignment.getHeight();
+ seqs = fullAlignment.getSequencesArray();
+ end = fullAlignment.getWidth();
}
else
{
.getCodonFrames();
if (codonMappings != null && !codonMappings.isEmpty())
{
- // fudge: check mappings are not protein-to-protein
- // TODO: nicer
- AlignedCodonFrame mapping = codonMappings.iterator().next();
- MapList[] mapLists = mapping.getdnaToProt();
- // mapLists can be empty if project load has not finished resolving seqs
- if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+ boolean doConsensus = false;
+ for (AlignedCodonFrame mapping : codonMappings)
+ {
+ // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+ MapList[] mapLists = mapping.getdnaToProt();
+ // mapLists can be empty if project load has not finished resolving
+ // seqs
+ if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+ {
+ doConsensus = true;
+ break;
+ }
+ }
+ if (doConsensus)
{
complementConsensus = new AlignmentAnnotation("cDNA Consensus",
"PID for cDNA", new Annotation[1], 0f, 100f,
}
@Override
- public Color getSequenceColour(SequenceI seq)
+ public ColorI getSequenceColour(SequenceI seq)
{
- Color sqc = sequenceColours.get(seq);
- return (sqc == null ? Color.white : sqc);
+ ColorI sqc = sequenceColours.get(seq);
+ return (sqc == null ? Colour.white : sqc);
}
@Override
- public void setSequenceColour(SequenceI seq, Color col)
+ public void setSequenceColour(SequenceI seq, ColorI col)
{
if (col == null)
{
* @see jalview.api.ViewStyleI#getTextColour()
*/
@Override
- public Color getTextColour()
+ public ColorI getTextColour()
{
return viewStyle.getTextColour();
}
* @see jalview.api.ViewStyleI#getTextColour2()
*/
@Override
- public Color getTextColour2()
+ public ColorI getTextColour2()
{
return viewStyle.getTextColour2();
}
* @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
*/
@Override
- public void setTextColour(Color textColour)
+ public void setTextColour(ColorI textColour)
{
viewStyle.setTextColour(textColour);
}
* @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
*/
@Override
- public void setTextColour2(Color textColour2)
+ public void setTextColour2(ColorI textColour2)
{
viewStyle.setTextColour2(textColour2);
}
* all gapped visible regions
*/
int lastSeq = alignment.getHeight() - 1;
+ List<AlignedCodonFrame> seqMappings = null;
for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
{
sequence = getAlignment().getSequenceAt(seqNo);
{
continue;
}
- List<AlignedCodonFrame> seqMappings = MappingUtils
- .findMappingsForSequence(sequence, mappings);
+ seqMappings = MappingUtils
+ .findMappingsForSequenceAndOthers(sequence, mappings,
+ getCodingComplement().getAlignment().getSequences());
if (!seqMappings.isEmpty())
{
break;
}
}
- if (sequence == null)
+ if (sequence == null || seqMappings == null || seqMappings.isEmpty())
{
/*
* No ungapped mapped sequence in middle column - do nothing
return 0;
}
MappingUtils.addSearchResults(sr, sequence,
- sequence.findPosition(middleColumn), mappings);
+ sequence.findPosition(middleColumn), seqMappings);
return seqOffset;
}
if (sg != null
&& (sgs = sg.getStartRes()) >= 0
&& sg.getStartRes() <= (sge = sg.getEndRes())
- && (colSel == null || colSel.getSelected() == null || colSel
- .getSelected().size() == 0))
+ && !this.hasSelectedColumns())
{
if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
{
}
}
}
+
+ /**
+ * hold status of current selection group - defined on alignment or not.
+ */
+ private boolean selectionIsDefinedGroup = false;
+
+ @Override
+ public boolean isSelectionDefinedGroup()
+ {
+ if (selectionGroup == null)
+ {
+ return false;
+ }
+ if (isSelectionGroupChanged(true))
+ {
+ selectionIsDefinedGroup = false;
+ List<SequenceGroup> gps = alignment.getGroups();
+ if (gps == null || gps.size() == 0)
+ {
+ selectionIsDefinedGroup = false;
+ }
+ else
+ {
+ selectionIsDefinedGroup = gps.contains(selectionGroup);
+ }
+ }
+ return selectionGroup.getContext() == alignment
+ || selectionIsDefinedGroup;
+ }
}
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureRenderer;
+import jalview.schemes.Colour;
import jalview.schemes.FeatureColour;
import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
- import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
import java.beans.PropertyChangeListener;
protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
this);
- protected AlignmentViewport av;
+ protected AlignViewportI av;
+ /*
+ * map holds per feature type, {{min, max}, {min, max}} feature score
+ * values for positional and non-positional features respectively
+ */
+ private Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+
@Override
public AlignViewportI getViewport()
{
renderOrder = neworder;
}
- protected Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
-
public Map<String, float[][]> getMinMax()
{
return minmax;
if (fc == null)
{
Color col = UserColourScheme.createColourFromName(featureType);
- fc = new FeatureColour(col);
+ fc = new FeatureColour(new Colour(col));
featureColours.put(featureType, fc);
}
return fc;
public Color getColour(SequenceFeature feature)
{
FeatureColourI fc = getFeatureStyle(feature.getType());
- return fc.getColor(feature);
+ return ColorUtils.getColor(fc.getColor(feature));
}
protected boolean showFeature(SequenceFeature sequenceFeature)
* note visible feature ordering and colours before update
*/
List<String> visibleFeatures = getDisplayedFeatureTypes();
- Map<String, Object> visibleColours = new HashMap<String, Object>(
+ Map<String, FeatureColourI> visibleColours = new HashMap<String, FeatureColourI>(
getFeatureColours());
FeaturesDisplayedI av_featuresdisplayed = null;
return renderOrder != null;
}
- /**
- * Returns feature types in ordering of rendering, where last means on top
- */
public List<String> getRenderOrder()
{
if (renderOrder == null)
* @return list of groups
*/
@Override
- public List getGroups(boolean visible)
+ public List<String> getGroups(boolean visible)
{
if (featureGroups != null)
{
return av.getFeaturesDisplayed();
}
- /**
- * Returns a (possibly empty) list of visible feature types, in render order
- * (last is on top)
- */
@Override
public List<String> getDisplayedFeatureTypes()
{
{
String[] renderOrder;
+ /*
+ * map of {groupName, isDisplayed}
+ */
Map<String, Boolean> featureGroups;
+ /*
+ * map of {featureType, colourScheme}
+ */
Map<String, FeatureColourI> featureColours;
float transparency;
{
String next = en.next();
FeatureColourI val = featureColours.get(next);
- // if (val instanceof GraduatedColor)
- if (val.isGraduatedColour() || val.isColourByLabel()) // why this test?
+ if (!val.isSimpleColour())
{
featureColours.put(next, new FeatureColour((FeatureColour) val));
}
import static org.testng.AssertJUnit.assertTrue;
import jalview.analysis.AlignSeq;
+import jalview.api.ColorI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.schemes.Colour;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.TaylorColourScheme;
- import jalview.structure.StructureViewSettings;
+ import jalview.structure.StructureImportSettings;
import java.awt.Color;
import java.util.Vector;
public void setUp()
{
System.out.println("setup");
- StructureViewSettings.setShowSeqFeatures(true);
+ StructureImportSettings.setShowSeqFeatures(true);
c = new PDBChain("1GAQ", "A");
}
c.makeBond(a2, a3);
c.setChainColours(Color.PINK);
assertEquals(2, c.bonds.size());
- assertEquals(Color.PINK, c.bonds.get(0).startCol);
- assertEquals(Color.PINK, c.bonds.get(0).endCol);
- assertEquals(Color.PINK, c.bonds.get(1).startCol);
- assertEquals(Color.PINK, c.bonds.get(1).endCol);
+ assertEquals(Colour.pink, c.bonds.get(0).startCol);
+ assertEquals(Colour.pink, c.bonds.get(0).endCol);
+ assertEquals(Colour.pink, c.bonds.get(1).startCol);
+ assertEquals(Colour.pink, c.bonds.get(1).endCol);
}
/**
@Test(groups = { "Functional" })
public void testSetChainColours_colourScheme()
{
- Color alaColour = new Color(204, 255, 0);
- Color glyColour = new Color(255, 153, 0);
+ ColorI alaColour = new Colour(204, 255, 0);
+ ColorI glyColour = new Colour(255, 153, 0);
a1.resName = "ALA";
a2.resName = "GLY";
a3.resName = "XXX"; // no colour defined
// bond a2 to a3 - no colour found for a3
// exception handling defaults to gray
b = c.bonds.get(2);
- assertEquals(Color.gray, b.startCol);
- assertEquals(Color.gray, b.endCol);
+ assertEquals(Colour.gray, b.startCol);
+ assertEquals(Colour.gray, b.endCol);
}
@Test(groups = { "Functional" })
public void testGetChargeColour()
{
- assertEquals(Color.red, PDBChain.getChargeColour("ASP"));
- assertEquals(Color.red, PDBChain.getChargeColour("GLU"));
- assertEquals(Color.blue, PDBChain.getChargeColour("LYS"));
- assertEquals(Color.blue, PDBChain.getChargeColour("ARG"));
- assertEquals(Color.yellow, PDBChain.getChargeColour("CYS"));
- assertEquals(Color.lightGray, PDBChain.getChargeColour("ALA"));
- assertEquals(Color.lightGray, PDBChain.getChargeColour(null));
+ assertEquals(Colour.red, PDBChain.getChargeColour("ASP"));
+ assertEquals(Colour.red, PDBChain.getChargeColour("GLU"));
+ assertEquals(Colour.blue, PDBChain.getChargeColour("LYS"));
+ assertEquals(Colour.blue, PDBChain.getChargeColour("ARG"));
+ assertEquals(Colour.yellow, PDBChain.getChargeColour("CYS"));
+ assertEquals(Colour.lightGray, PDBChain.getChargeColour("ALA"));
+ assertEquals(Colour.lightGray, PDBChain.getChargeColour(null));
}
/**
assertEquals(3, c.bonds.size());
// bond a1 to a2
Bond b = c.bonds.get(0);
- assertEquals(Color.red, b.startCol);
- assertEquals(Color.blue, b.endCol);
+ assertEquals(Colour.red, b.startCol);
+ assertEquals(Colour.blue, b.endCol);
// bond a2 to a3
b = c.bonds.get(1);
- assertEquals(Color.blue, b.startCol);
- assertEquals(Color.yellow, b.endCol);
+ assertEquals(Colour.blue, b.startCol);
+ assertEquals(Colour.yellow, b.endCol);
// bond a3 to a4
b = c.bonds.get(2);
- assertEquals(Color.yellow, b.startCol);
- assertEquals(Color.lightGray, b.endCol);
+ assertEquals(Colour.yellow, b.startCol);
+ assertEquals(Colour.lightGray, b.endCol);
}
/**
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
++import jalview.schemes.Colour;
import jalview.util.MapList;
--import java.awt.Color;
import java.util.List;
import org.testng.annotations.AfterClass;
public class EnsemblGeneTest
{
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public void tearDown()
{
SequenceOntologyFactory.setInstance(null);
assertTrue(fc.isFeatureDisplayed("sequence_variant"));
assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
assertFalse(fc.isFeatureDisplayed("transcript"));
-- assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
++ assertEquals(Colour.red, fc.getFeatureColour("sequence_variant")
.getColour());
-- assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
++ assertEquals(Colour.red, fc.getFeatureColour("feature_variant")
.getColour());
assertTrue(fc.getFeatureColour("exon").isColourByLabel());
assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
import static org.testng.AssertJUnit.assertTrue;
import jalview.api.FeatureColourI;
+ import jalview.api.FeatureRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.schemes.Colour;
-import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.util.Map;
*/
colours = af.getFeatureRenderer().getFeatureColours();
assertEquals("26 feature group colours not found", 26, colours.size());
- assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
- assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
+ assertEquals(colours.get("Cath").getColour(), new Colour(0x93b1d1));
+ assertEquals(colours.get("ASX-MOTIF").getColour(), new Colour(0x6addbb));
/*
* verify (some) features on sequences
*/
SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures(); // FER_CAPAA
- assertEquals(7, sfs.length);
+ assertEquals(8, sfs.length);
SequenceFeature sf = sfs[0];
+ assertEquals("Pfam family%LINK%", sf.description);
+ assertEquals(0, sf.begin);
+ assertEquals(0, sf.end);
+ assertEquals("uniprot", sf.featureGroup);
+ assertEquals("Pfam", sf.type);
+ assertEquals(1, sf.links.size());
+ assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
+ sf.links.get(0));
+
+ sf = sfs[1];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(39, sf.begin);
assertEquals(39, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[1];
+ sf = sfs[2];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(44, sf.begin);
assertEquals(44, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[2];
+ sf = sfs[3];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(47, sf.begin);
assertEquals(47, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[3];
+ sf = sfs[4];
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(77, sf.begin);
assertEquals(77, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
- sf = sfs[4];
+ sf = sfs[5];
assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
sf.description);
- assertEquals("Pfam 8_8|http://pfam.sanger.ac.uk/family/PF00111",
- sf.links.get(0).toString());
+ assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
+ sf.links.get(0));
assertEquals(8, sf.begin);
assertEquals(83, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("Pfam", sf.type);
- sf = sfs[5];
+ sf = sfs[6];
assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
assertEquals(3, sf.begin);
assertEquals(93, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("Cath", sf.type);
- sf = sfs[6];
+ sf = sfs[7];
assertEquals(
"High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
sf.description);
assertEquals(
"PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
- sf.links.get(0).toString());
+ sf.links.get(0));
assertEquals(89, sf.begin);
assertEquals(89, sf.end);
assertEquals("netphos", sf.featureGroup);
// verify colours read or synthesized
colours = af.getFeatureRenderer().getFeatureColours();
assertEquals("1 feature group colours not found", 1, colours.size());
- assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
+ assertEquals(colours.get("METAL").getColour(), new Colour(0xcc9900));
// verify feature on FER_CAPAA
SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
}
/**
+ * Test various ways of describing a feature colour scheme
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testParseGraduatedColourScheme() throws Exception
+ {
+ FeaturesFile ff = new FeaturesFile();
+
+ // colour by label:
+ FeatureColourI gc = ff.parseGraduatedColourScheme(
+ "BETA-TURN-IR\t9a6a94", "label");
+ assertTrue(gc.isColourByLabel());
+ assertEquals(Colour.white, gc.getMinColour());
+ assertEquals(Colour.black, gc.getMaxColour());
+ assertTrue(gc.isAutoScaled());
+
+ // using colour name, rgb, etc:
+ String spec = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
+ gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
+ assertFalse(gc.isColourByLabel());
+ assertEquals(Colour.blue, gc.getMinColour());
+ assertEquals(new Colour(255, 0, 255), gc.getMaxColour());
+ assertFalse(gc.isAutoScaled());
+ // assertFalse(gc.getTolow());
+ assertEquals(20.0f, gc.getMin(), 0.001f);
+ assertEquals(95.0f, gc.getMax(), 0.001f);
+ assertTrue(gc.isBelowThreshold());
+ assertEquals(66.0f, gc.getThreshold(), 0.001f);
+
+ // inverse gradient high to low:
+ spec = "blue|255,0,255|95.0|20.0|below|66.0";
+ gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
+ assertTrue(gc.isAutoScaled());
+ // assertTrue(gc..getTolow());
+ }
+
+ /**
* Test parsing a features file with GFF formatted content only
*
* @throws Exception
parseResult);
checkDatasetfromSimpleGff3(dataset);
}
+
+ @Test(groups = { "Functional" })
+ public void testPrintJalviewFormat() throws Exception
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
+ .getFeatureColours();
+ String features = "METAL\tcc9900\n"
+ + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
+ + "Pfam\tred\n"
+ + "STARTGROUP\tuniprot\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
+ + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
+ + "ENDGROUP\tuniprot\n";
+ FeaturesFile featuresFile = new FeaturesFile(features,
+ FormatAdapter.PASTE);
+ featuresFile.parse(al.getDataset(), colours, false);
+
+ /*
+ * first with no features displayed
+ */
+ FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
+ Map<String, FeatureColourI> visible = fr
+ .getDisplayedFeatureCols();
+ String exported = featuresFile.printJalviewFormat(
+ al.getSequencesArray(), visible);
+ String expected = "No Features Visible";
+ assertEquals(expected, exported);
+
+ /*
+ * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
+ */
+ fr.setVisible("METAL");
+ fr.setVisible("GAMMA-TURN");
+ visible = fr.getDisplayedFeatureCols();
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
+ visible);
+ expected = "METAL\tcc9900\n"
+ + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+ + "\nSTARTGROUP\tuniprot\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+ + "ENDGROUP\tuniprot\n";
+ assertEquals(expected, exported);
+
+ /*
+ * now set Pfam visible
+ */
+ fr.setVisible("Pfam");
+ visible = fr.getDisplayedFeatureCols();
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
+ visible);
+ /*
+ * note the order of feature types is uncontrolled - derives from
+ * FeaturesDisplayed.featuresDisplayed which is a HashSet
+ */
+ expected = "METAL\tcc9900\n"
+ + "Pfam\tff0000\n"
+ + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+ + "\nSTARTGROUP\tuniprot\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+ + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+ + "ENDGROUP\tuniprot\n";
+ assertEquals(expected, exported);
+ }
}
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;
+import jalview.api.ColorI;
import jalview.datamodel.SequenceFeature;
import jalview.util.Format;
public class FeatureColourTest
{
@Test(groups = { "Functional" })
- public void testCopyConstructor()
- {
- /*
- * plain colour
- */
- FeatureColour fc = new FeatureColour(Color.RED);
- FeatureColour fc1 = new FeatureColour(fc);
- assertTrue(fc1.getColour().equals(Color.RED));
- assertFalse(fc1.isGraduatedColour());
- assertFalse(fc1.isColourByLabel());
-
- /*
- * min-max colour
- */
- fc = new FeatureColour(Color.gray, Color.black, 10f, 20f);
- fc.setAboveThreshold(true);
- fc.setThreshold(12f);
- fc1 = new FeatureColour(fc);
- assertTrue(fc1.isGraduatedColour());
- assertFalse(fc1.isColourByLabel());
- assertTrue(fc1.isAboveThreshold());
- assertEquals(12f, fc1.getThreshold());
- assertEquals(Color.gray, fc1.getMinColour());
- assertEquals(Color.black, fc1.getMaxColour());
- assertEquals(10f, fc1.getMin());
- assertEquals(20f, fc1.getMax());
-
- /*
- * colour by label
- */
- fc = new FeatureColour();
- fc.setColourByLabel(true);
- fc1 = new FeatureColour(fc);
- assertTrue(fc1.isColourByLabel());
- assertFalse(fc1.isGraduatedColour());
- }
-
- @Test(groups = { "Functional" })
public void testIsColored_simpleColour()
{
FeatureColour fc = new FeatureColour(Color.RED);
public void testIsColored_aboveThreshold()
{
// graduated colour range from score 20 to 100
- FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 20f,
- 100f);
+ FeatureColour fc = new FeatureColour(new Colour(Color.WHITE),
+ new Colour(Color.BLACK), 20f, 100f);
// score 0 is adjusted to bottom of range
SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 0f,
null);
assertTrue(fc.isColored(sf));
- assertEquals(Color.WHITE, fc.getColor(sf));
+ assertEquals(fc.getColor(sf), Colour.white);
// score 120 is adjusted to top of range
sf.setScore(120f);
- assertEquals(Color.BLACK, fc.getColor(sf));
+ assertEquals(fc.getColor(sf), Colour.black);
// value below threshold is still rendered
// setting threshold has no effect yet...
fc.setThreshold(60f);
sf.setScore(36f);
assertTrue(fc.isColored(sf));
- assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+ assertEquals(fc.getColor(sf), new Colour(204, 204, 204));
// now apply threshold:
fc.setAboveThreshold(true);
assertFalse(fc.isColored(sf));
// colour is still returned though ?!?
- assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+ assertEquals(fc.getColor(sf), new Colour(204, 204, 204));
sf.setScore(84); // above threshold now
assertTrue(fc.isColored(sf));
- assertEquals(new Color(51, 51, 51), fc.getColor(sf));
+ assertEquals(fc.getColor(sf), new Colour(51, 51, 51));
}
@Test(groups = { "Functional" })
public void testGetColor_simpleColour()
{
- FeatureColour fc = new FeatureColour(Color.RED);
- assertEquals(Color.RED, fc.getColor(new SequenceFeature()));
+ FeatureColour fc = new FeatureColour(Colour.red);
+ assertEquals(fc.getColor(new SequenceFeature()), Colour.red);
}
@Test(groups = { "Functional" })
fc.setColourByLabel(true);
SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
null);
- Color expected = UserColourScheme.createColourFromName("desc");
- assertEquals(expected, fc.getColor(sf));
+ ColorI expected = new Colour(
+ UserColourScheme.createColourFromName("desc"));
+ assertEquals(fc.getColor(sf), expected);
+ // assertEquals(expected, fc.getColor(sf));
}
@Test(groups = { "Functional" })
float red = 128 / 255f + 3 / 4f * (255 - 128) / 255f;
float green = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
float blue = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
- Color expected = new Color(red, green, blue);
- assertEquals(expected, fc.getColor(sf));
+ Colour expected = new Colour(red, green, blue);
+ assertEquals(fc.getColor(sf), expected);
+ // assertEquals(expected, fc.getColor(sf));
}
@Test(groups = { "Functional" })
null);
fc.setThreshold(100f); // ignore for now
assertTrue(fc.isColored(sf));
- assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+ assertEquals(fc.getColor(sf), new Colour(204, 204, 204));
+ // assertEquals(new Color(204, 204, 204), fc.getColor(sf));
fc.setAboveThreshold(true); // feature lies below threshold
assertFalse(fc.isColored(sf));
- assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+ assertEquals(fc.getColor(sf), new Colour(204, 204, 204));
+ // assertEquals(new Color(204, 204, 204), fc.getColor(sf));
}
/**
*/
fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f);
String greenHex = Format.getHexString(Color.GREEN);
- String expected = String.format("domain\t%s|%s|12.0|25.0|none",
+ String expected = String.format("domain\t%s|%s|abso|12.0|25.0|none",
greenHex, redHex);
assertEquals(expected, fc.toJalviewFormat("domain"));
* colour ranges over the actual score ranges (not min/max)
*/
fc.setAutoScaled(true);
- expected = String.format("domain\t%s|%s|abso|12.0|25.0|none", greenHex,
+ expected = String.format("domain\t%s|%s|12.0|25.0|none", greenHex,
redHex);
assertEquals(expected, fc.toJalviewFormat("domain"));
*/
fc.setThreshold(12.5f);
fc.setBelowThreshold(true);
- expected = String.format("domain\t%s|%s|abso|12.0|25.0|below|12.5",
+ expected = String.format("domain\t%s|%s|12.0|25.0|below|12.5",
greenHex, redHex);
assertEquals(expected, fc.toJalviewFormat("domain"));
*/
fc.setThreshold(12.5f);
fc.setAboveThreshold(true);
+ fc.setAutoScaled(false);
expected = String.format("domain\t%s|%s|abso|12.0|25.0|above|12.5",
greenHex, redHex);
assertEquals(expected, fc.toJalviewFormat("domain"));
*/
FeatureColour fc = FeatureColour.parseJalviewFeatureColour("red");
assertTrue(fc.isSimpleColour());
- assertEquals(Color.RED, fc.getColour());
+ assertEquals(fc.getColour(), Colour.red);
/*
* simple colour by hex code
fc = FeatureColour.parseJalviewFeatureColour(Format
.getHexString(Color.RED));
assertTrue(fc.isSimpleColour());
- assertEquals(Color.RED, fc.getColour());
+ assertEquals(fc.getColour(), Colour.red);
+ // assertEquals(Color.RED, fc.getColour());
/*
* simple colour by rgb triplet
*/
fc = FeatureColour.parseJalviewFeatureColour("255,0,0");
assertTrue(fc.isSimpleColour());
- assertEquals(Color.RED, fc.getColour());
+ assertEquals(fc.getColour(), Colour.red);
+ // assertEquals(Color.RED, fc.getColour());
/*
* malformed colour
fc = FeatureColour.parseJalviewFeatureColour("red|green|10.0|20.0");
assertTrue(fc.isGraduatedColour());
assertFalse(fc.hasThreshold());
- assertEquals(Color.RED, fc.getMinColour());
- assertEquals(Color.GREEN, fc.getMaxColour());
+ assertEquals(fc.getMinColour(), Colour.red);
+ // assertEquals(Color.RED, fc.getMinColour());
+ assertEquals(fc.getMaxColour(), Colour.green);
+ // assertEquals(Color.GREEN, fc.getMaxColour());
assertEquals(10f, fc.getMin());
assertEquals(20f, fc.getMax());
assertTrue(fc.isAutoScaled());
assertTrue(fc.hasThreshold());
assertTrue(fc.isAboveThreshold());
assertEquals(15f, fc.getThreshold());
- assertEquals(Color.RED, fc.getMinColour());
- assertEquals(Color.GREEN, fc.getMaxColour());
+ assertEquals(fc.getMinColour(), Colour.red);
+ // assertEquals(Color.RED, fc.getMinColour());
+ assertEquals(fc.getMaxColour(), Colour.green);
+ // assertEquals(Color.GREEN, fc.getMaxColour());
assertEquals(10f, fc.getMin());
assertEquals(20f, fc.getMax());
assertTrue(fc.isAutoScaled());
assertTrue(fc.hasThreshold());
assertTrue(fc.isBelowThreshold());
assertEquals(15f, fc.getThreshold());
- assertEquals(Color.RED, fc.getMinColour());
- assertEquals(Color.GREEN, fc.getMaxColour());
+ assertEquals(fc.getMinColour(), Colour.red);
+ // assertEquals(Color.RED, fc.getMinColour());
+ assertEquals(fc.getMaxColour(), Colour.green);
+ // assertEquals(Color.GREEN, fc.getMaxColour());
assertEquals(10f, fc.getMin());
assertEquals(20f, fc.getMax());
-
- descriptor = String
- .format("blue|255,0,255|absolute|20.0|95.0|below|66.0");
- fc = FeatureColour.parseJalviewFeatureColour(descriptor);
- assertTrue(fc.isGraduatedColour());
}
}
git://source.jalview.org / jalview.git / commitdiff