import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.MouseMotionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
+import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Enumeration;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import java.util.Vector;
public class FeatureSettings extends Panel implements ItemListener,
MouseListener, MouseMotionListener, ActionListener,
// Group selection states
void resetTable(boolean groupsChanged)
{
- SequenceFeature[] tmpfeatures;
- String group = null, type;
- Vector<String> visibleChecks = new Vector<String>();
+ List<String> displayableTypes = new ArrayList<String>();
Set<String> foundGroups = new HashSet<String>();
+
AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
- if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
- {
- continue;
- }
+ SequenceI seq = alignment.getSequenceAt(i);
- tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
- int index = 0;
- while (index < tmpfeatures.length)
+ /*
+ * get the sequence's groups for positional features
+ * and keep track of which groups are visible
+ */
+ Set<String> groups = seq.getFeatures().getFeatureGroups(true);
+ Set<String> visibleGroups = new HashSet<String>();
+ for (String group : groups)
{
- group = tmpfeatures[index].featureGroup;
- foundGroups.add(group);
-
+ // if (group == null || fr.checkGroupVisibility(group, true))
if (group == null || checkGroupState(group))
{
- type = tmpfeatures[index].getType();
- if (!visibleChecks.contains(type))
- {
- visibleChecks.addElement(type);
- }
+ visibleGroups.add(group);
}
- index++;
}
+ foundGroups.addAll(groups);
+
+ /*
+ * get distinct feature types for visible groups
+ * record distinct visible types
+ */
+ Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true,
+ visibleGroups.toArray(new String[visibleGroups.size()]));
+ displayableTypes.addAll(types);
}
/*
{
comps = featurePanel.getComponents();
check = (MyCheckbox) comps[i];
- if (!visibleChecks.contains(check.type))
+ if (!displayableTypes.contains(check.type))
{
featurePanel.remove(i);
cSize--;
{
String item = rol.get(ro);
- if (!visibleChecks.contains(item))
+ if (!displayableTypes.contains(item))
{
continue;
}
- visibleChecks.removeElement(item);
+ displayableTypes.remove(item);
addCheck(false, item);
}
}
- // now add checkboxes which should be visible,
- // if they have not already been added
- Enumeration<String> en = visibleChecks.elements();
-
- while (en.hasMoreElements())
+ /*
+ * now add checkboxes which should be visible,
+ * if they have not already been added
+ */
+ for (String type : displayableTypes)
{
- addCheck(groupsChanged, en.nextElement().toString());
+ addCheck(groupsChanged, type);
}
featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
Checkbox check = (Checkbox) featurePanel.getComponent(i);
check.setState(!check.getState());
}
- selectionChanged();
+ selectionChanged(true);
}
private ItemListener groupItemListener = new ItemListener()
@Override
public void itemStateChanged(ItemEvent evt)
{
- selectionChanged();
+ selectionChanged(true);
}
- void selectionChanged()
+ void selectionChanged(boolean updateOverview)
{
Component[] comps = featurePanel.getComponents();
int cSize = comps.length;
fr.setFeaturePriority(data);
- ap.paintAlignment(true);
+ ap.paintAlignment(updateOverview);
}
MyCheckbox selectedCheck;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
-import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import java.awt.Color;
import java.io.File;
import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import org.testng.annotations.BeforeClass;
* updated - JAL-1904), and verify (some) feature group colours
*/
colours = af.getFeatureRenderer().getFeatureColours();
- assertEquals("26 feature group colours not found", 26, colours.size());
+ assertEquals("27 feature group colours not found", 27, colours.size());
assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
+ FeatureColourI kdColour = colours.get("kdHydrophobicity");
+ assertTrue(kdColour.isGraduatedColour());
+ assertTrue(kdColour.isAboveThreshold());
+ assertEquals(-2f, kdColour.getThreshold());
/*
* verify (some) features on sequences
*/
- SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
+ List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures(); // FER_CAPAA
- assertEquals(8, sfs.length);
- SequenceFeature sf = sfs[0];
+ SequenceFeatures.sortFeatures(sfs, true);
+ assertEquals(8, sfs.size());
+
+ /*
+ * verify (in ascending start position order)
+ */
+ SequenceFeature sf = sfs.get(0);
assertEquals("Pfam family%LINK%", sf.description);
assertEquals(0, sf.begin);
assertEquals(0, sf.end);
assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
sf.links.get(0));
- sf = sfs[1];
+ sf = sfs.get(1);
+ 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.get(2);
+ assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
+ sf.description);
+ 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.get(3);
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[2];
+
+ sf = sfs.get(4);
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[3];
+
+ sf = sfs.get(5);
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[4];
+
+ sf = sfs.get(6);
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[5];
- assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
- sf.description);
- 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[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[7];
+
+ sf = sfs.get(7);
assertEquals(
"High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
sf.description);
assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
// verify feature on FER_CAPAA
- SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
+ List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures();
- assertEquals(1, sfs.length);
- SequenceFeature sf = sfs[0];
+ assertEquals(1, sfs.size());
+ SequenceFeature sf = sfs.get(0);
assertEquals("Iron-sulfur,2Fe-2S", sf.description);
assertEquals(44, sf.begin);
assertEquals(45, sf.end);
// verify feature on FER1_SOLLC
sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
- assertEquals(1, sfs.length);
- sf = sfs[0];
+ assertEquals(1, sfs.size());
+ sf = sfs.get(0);
assertEquals("uniprot", sf.description);
assertEquals(55, sf.begin);
assertEquals(130, sf.end);
featuresFile.parse(al.getDataset(), colours, true));
// verify feature on FER_CAPAA
- SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
+ List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures();
- assertEquals(1, sfs.length);
- SequenceFeature sf = sfs[0];
+ assertEquals(1, sfs.size());
+ SequenceFeature sf = sfs.get(0);
// description parsed from Note attribute
assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
assertEquals(39, sf.begin);
// verify feature on FER1_SOLLC1
sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
- assertEquals(1, sfs.length);
- sf = sfs[0];
+ assertEquals(1, sfs.size());
+ sf = sfs.get(0);
// ID used for description if available
assertEquals("$23", sf.description);
assertEquals(55, sf.begin);
featuresFile.parse(al.getDataset(), colours, true));
// verify FER_CAPAA feature
- SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
+ List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures();
- assertEquals(1, sfs.length);
- SequenceFeature sf = sfs[0];
+ assertEquals(1, sfs.size());
+ SequenceFeature sf = sfs.get(0);
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(39, sf.begin);
assertEquals(39, sf.end);
// verify FER1_SOLLC feature
sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
- assertEquals(1, sfs.length);
- sf = sfs[0];
+ assertEquals(1, sfs.size());
+ sf = sfs.get(0);
assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
assertEquals(86, sf.begin);
assertEquals(87, sf.end);
assertFalse("dummy replacement buggy for seq2",
placeholderseq.equals(seq2.getSequenceAsString()));
assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
- assertEquals("Wrong number of features", 3,
- seq1.getSequenceFeatures().length);
- assertNull(seq2.getSequenceFeatures());
+ assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
+ .size());
+ assertTrue(seq2.getSequenceFeatures().isEmpty());
assertEquals(
"Wrong number of features",
0,
seq2.getSequenceFeatures() == null ? 0 : seq2
- .getSequenceFeatures().length);
+ .getSequenceFeatures().size());
assertTrue(
"Expected at least one CDNA/Protein mapping for seq1",
dataset.getCodonFrame(seq1) != null
+ "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
+ "Pfam\tred\n"
+ "STARTGROUP\tuniprot\n"
+ + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
+ "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"
featuresFile.parse(al.getDataset(), colours, false);
/*
- * first with no features displayed
+ * add positional and non-positional features with null and
+ * empty feature group to check handled correctly
+ */
+ SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
+ seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
+ null));
+ seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
+ Float.NaN, null));
+ seq = al.getSequenceAt(2); // FER1_SOLLC
+ seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
+ Float.NaN, ""));
+ seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
+ -2.6f, ""));
+
+ /*
+ * first with no features displayed, exclude non-positional features
*/
FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
+ List<String> visibleGroups = new ArrayList<String>(
+ Arrays.asList(new String[] {}));
String exported = featuresFile.printJalviewFormat(
- al.getSequencesArray(), visible);
+ al.getSequencesArray(), visible, visibleGroups, false);
String expected = "No Features Visible";
assertEquals(expected, exported);
/*
+ * include non-positional features
+ */
+ visibleGroups.add("uniprot");
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
+ visible, visibleGroups, true);
+ expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
+ + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
+ + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output
+ + "\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n";
+ 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);
+ visible, visibleGroups, false);
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"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ "ENDGROUP\tuniprot\n";
assertEquals(expected, exported);
fr.setVisible("Pfam");
visible = fr.getDisplayedFeatureCols();
exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
- visible);
+ visible, visibleGroups, false);
/*
- * note the order of feature types is uncontrolled - derives from
- * FeaturesDisplayed.featuresDisplayed which is a HashSet
+ * features are output within group, ordered by sequence and by type
*/
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"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\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";
+ + "ENDGROUP\tuniprot\n"
+ // null / empty group features output after features in named
+ // groups:
+ + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
+ + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
+ assertEquals(expected, exported);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testPrintGffFormat() throws Exception
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+
+ /*
+ * no features
+ */
+ FeaturesFile featuresFile = new FeaturesFile();
+ FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
+ Map<String, FeatureColourI> visible = new HashMap<String, FeatureColourI>();
+ List<String> visibleGroups = new ArrayList<String>(
+ Arrays.asList(new String[] {}));
+ String exported = featuresFile.printGffFormat(al.getSequencesArray(),
+ visible, visibleGroups, false);
+ String gffHeader = "##gff-version 2\n";
+ assertEquals(gffHeader, exported);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+ visibleGroups, true);
+ assertEquals(gffHeader, exported);
+
+ /*
+ * add some features
+ */
+ al.getSequenceAt(0).addSequenceFeature(
+ new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
+ al.getSequenceAt(0).addSequenceFeature(
+ new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
+ al.getSequenceAt(1)
+ .addSequenceFeature(
+ new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
+ "s3dm"));
+ SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
+ "Uniprot");
+ sf.setAttributes("x=y;black=white");
+ sf.setStrand("+");
+ sf.setPhase("2");
+ al.getSequenceAt(1).addSequenceFeature(sf);
+
+ /*
+ * with no features displayed, exclude non-positional features
+ */
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+ visibleGroups, false);
+ assertEquals(gffHeader, exported);
+
+ /*
+ * include non-positional features
+ */
+ visibleGroups.add("Uniprot");
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+ visibleGroups, true);
+ String expected = gffHeader
+ + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
+ * only Uniprot group visible here...
+ */
+ fr.setVisible("METAL");
+ fr.setVisible("GAMMA-TURN");
+ visible = fr.getDisplayedFeatureCols();
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+ visibleGroups, false);
+ // METAL feature has null group: description used for column 2
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * set s3dm group visible
+ */
+ visibleGroups.add("s3dm");
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+ visibleGroups, false);
+ // METAL feature has null group: description used for column 2
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * now set Pfam visible
+ */
+ fr.setVisible("Pfam");
+ visible = fr.getDisplayedFeatureCols();
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+ visibleGroups, false);
+ // Pfam feature columns include strand(+), phase(2), attributes
+ expected = gffHeader
+ + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
+ + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
assertEquals(expected, exported);
}
}
git://source.jalview.org / jalview.git / commitdiff