BioJS viewer

Jalview local Jnlp File

-<jnlp spec="1.0+" codebase="http://www.jalview.org/webstart/"> - <information> - <title>Jalview</title> - <vendor>The Barton Group</vendor> - <homepage href="http://www.jalview.org"/> - <description>Jalview Multiple Alignment Editor</description> - <description kind="short">Jalview</description> - <icon href="http://www.jalview.org/webstart/logo_big.gif" kind="default"/> - <association extensions="fa" mime-type="application-x/ext-file"/> - <association extensions="fasta" mime-type="application-x/ext-file"/> - <association extensions="fastq" mime-type="application-x/ext-file"/> - <association extensions="blc" mime-type="application-x/ext-file"/> - <association extensions="msf" mime-type="application-x/ext-file"/> - <association extensions="pfam" mime-type="application-x/ext-file"/> - <association extensions="aln" mime-type="application-x/ext-file"/> - <association extensions="pir" mime-type="application-x/ext-file"/> - <association extensions="stk" mime-type="application-x/ext-file"/> - <offline-allowed/> - </information> - <security> - <all-permissions/> - </security> - <resources> -  - <j2se version="1.5+" initial-heap-size="500M" max-heap-size="1000M"/> - <jar href="jalview.jar"/> - <jar href="JGoogleAnalytics-0.2.1-SNAPSHOT.jar"/> - <jar href="Jmol-12.1.13.jar"/> - <jar href="activation.jar"/> - <jar href="axis.jar"/> - <jar href="castor-1.1-cycle-xml.jar"/> - <jar href="commons-discovery.jar"/> - <jar href="commons-logging.jar"/> - <jar href="jaxrpc.jar"/> - <jar href="jhall.jar"/> - <jar href="log4j-1.2.8.jar"/> - <jar href="mail.jar"/> - <jar href="min-jaba-client.jar"/> - <jar href="regex.jar"/> - <jar href="saaj.jar"/> - <jar href="vamsas-client.jar"/> - <jar href="wsdl4j.jar"/> - <jar href="xercesImpl.jar"/> - <jar href="xml-apis.jar"/> - <property name="jalview.version" value="2.6.1"/> - </resources> - <application-desc main-class="jalview.bin.Jalview"/> -</jnlp> -

Web Start Version -

JavaWS sets the JVM parameters through special tags in the JNLP file. You'll - need to make your own jnlp file and add the following parameter into the - <resources> element. -

-<j2se version="1.5+" initial-heap-size="500M" max-heap-size="1000M"/>
-

- Save the jnlp file somewhere and then - if you start Jalview through your - web browser, point your browser at the file's url, othewise simply run javaws - with the file location as its argument. The file's url is something like :
-

+		Web Start Version
+			
+				JavaWS sets the JVM parameters through special tags in the JNLP
+				file. You can obtain a JNLP file with modified memory settings from
+				our service with the following link (replace 2G with desired memory
+				in G or M):
 http://www.jalview.org/services/launchApp?jvm-max-heap=2G
+			
+			
+				Alternatively, if you want to create your own JNLP file then please
+				download the latest JNLP file from http://www.jalview.org/webstart/jalview.jnlp
+				and modify the max-heap-size parameter for the j2se tag in the
+				<resources> element. e.g.
+			
+<j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/>
+ In both cases, you should save your new jnlp file somewhere and
+			then either point your web browser at the file's url, launch it from
+			your file browser, or from a terminal window run javaws (located in
+			your Java installation's bin directory) with the file location as its
+			argument. The file's url is something like :
  file://<full path to file>
-
-    If jalview doesn't start up, see below. You'll have
-    to edit the above settings in the JNLP file using a text editor, save it,
-    and try starting Jalview with it once more.
-    
-  Install Anywhere version
+

If jalview doesn't start up, see below. + You'll have to edit the above settings in the JNLP file using a text + editor, save it, and try starting Jalview with it once more. +

Install Anywhere version

You need to change the InstallAnywhere configuration settings for the application. These are found in different places depending upon which operating system you have : diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index f67faa9..95dcad8 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -62,18 +62,16 @@ Select the format of the text by selecting one of the following menu items.

FASTA -
MSF -
CLUSTAL -
BLC -
PIR -
PFAM -
FASTA
MSF
CLUSTAL
BLC
PIR
PFAM
PileUp
AMSA
STH
Phylip

Print (Control P)
Jalview will print the alignment using the current fonts and colours of @@ -203,9 +201,9 @@ the last redundancy deletion.

Pad Gaps
When selected, - the alignment will be kept at minimal width (so there no empty + the alignment will be kept at minimal width (so there are no empty columns before or after the first or last aligned residue) and all - sequences will be padded with gap characters to the before and + sequences will be padded with gap characters before and after their terminating residues.
This switch is useful when making a tree using unaligned sequences and when working with alignment analysis programs which require 'properly aligned diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html index e44f3ac..67b3d2e 100755 --- a/help/html/menus/alwedit.html +++ b/help/html/menus/alwedit.html @@ -91,8 +91,8 @@ undo the last redundancy deletion.

Pad Gaps
When selected, the alignment will be kept at minimal width (so - there no empty columns before or after the first or last aligned - residue) and all sequences will be padded with gap characters to the + there are no empty columns before or after the first or last aligned + residue) and all sequences will be padded with gap characters before and after their terminating residues.
This switch is useful when making a tree using unaligned sequences and when working with alignment analysis programs which require 'properly diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html index 7cd096c..bf459e3 100755 --- a/help/html/menus/alwfile.html +++ b/help/html/menus/alwfile.html @@ -61,6 +61,10 @@

BLC

PIR

PFAM
+
PileUp
+
AMSA
+
STH
+
Phylip

+ * Build a data structure which maps contiguous subsequences for each colour. + * This generates a data structure from which we can easily generate the + * Chimera command for colour by sequence. + * Color + * Model number + * Chain + * list of start/end ranges + * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains) + *

" - + "

"); - htmlSvg.append(titleSvg); - htmlSvg.append("

").append(alignmentSvg); + htmlSvg.append("" + + ""); + htmlSvg.append("

"); + htmlSvg.append( +"

") + .append(titleSvg) + .append("

") + .append("

\n\n\n\n"); + htmlSvg.append( +"

"); + htmlSvg.append( + "

") + .append(alignmentSvg) +.append("

") + .append("

"); htmlSvg.append("

"); + + htmlSvg.append("\n" + + "\n" + + ""); + return htmlSvg.toString(); } } diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index 9c7478b..4fb2516 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -136,8 +136,14 @@ public class IdentifyFile break; } + // if (data.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>")) + if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>")) + { + reply = "HTML"; + break; + } - if ((data.indexOf("<") > -1)) + if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>")) { reply = "RNAML"; @@ -275,6 +281,7 @@ public class IdentifyFile break; } + /* * // TODO comment out SimpleBLAST identification for Jalview 2.4.1 else * if (!lineswereskipped && data.indexOf("BLAST")<4) { reply = @@ -320,6 +327,7 @@ public class IdentifyFile public static void main(String[] args) { + for (int i = 0; args != null && i < args.length; i++) { IdentifyFile ider = new IdentifyFile(); diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 6fba9c6..1757239 100644 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@ -22,6 +22,7 @@ package jalview.io; import java.util.ArrayList; import java.util.Hashtable; +import java.util.List; import java.util.Vector; import jalview.datamodel.DBRefEntry; @@ -54,30 +55,30 @@ public class SequenceAnnotationReport * TODO refactor to Jalview 'utilities' somehow. */ public void appendFeatures(final StringBuffer tooltipText2, int rpos, - SequenceFeature[] features) + List features) { appendFeatures(tooltipText2, rpos, features, null); } public void appendFeatures(final StringBuffer tooltipText2, int rpos, - SequenceFeature[] features, Hashtable minmax) + List features, Hashtable minmax) { String tmpString; if (features != null) { - for (int i = 0; i < features.length; i++) + for (SequenceFeature feature:features) { - if (features[i].getType().equals("disulfide bond")) + if (feature.getType().equals("disulfide bond")) { - if (features[i].getBegin() == rpos - || features[i].getEnd() == rpos) + if (feature.getBegin() == rpos + || feature.getEnd() == rpos) { if (tooltipText2.length() > 6) { tooltipText2.append("
"); } - tooltipText2.append("disulfide bond " + features[i].getBegin() - + ":" + features[i].getEnd()); + tooltipText2.append("disulfide bond " + feature.getBegin() + + ":" + feature.getEnd()); } } else @@ -87,25 +88,25 @@ public class SequenceAnnotationReport tooltipText2.append("
"); } // TODO: remove this hack to display link only features - boolean linkOnly = features[i].getValue("linkonly") != null; + boolean linkOnly = feature.getValue("linkonly") != null; if (!linkOnly) { - tooltipText2.append(features[i].getType() + " "); + tooltipText2.append(feature.getType() + " "); if (rpos != 0) { // we are marking a positional feature - tooltipText2.append(features[i].begin); + tooltipText2.append(feature.begin); } - if (features[i].begin != features[i].end) + if (feature.begin != feature.end) { - tooltipText2.append(" " + features[i].end); + tooltipText2.append(" " + feature.end); } - if (features[i].getDescription() != null - && !features[i].description.equals(features[i] + if (feature.getDescription() != null + && !feature.description.equals(feature .getType())) { - tmpString = features[i].getDescription(); + tmpString = feature.getDescription(); String tmp2up = tmpString.toUpperCase(); int startTag = tmp2up.indexOf(""); if (startTag > -1) @@ -150,27 +151,27 @@ public class SequenceAnnotationReport } } // check score should be shown - if (features[i].getScore() != Float.NaN) + if (feature.getScore() != Float.NaN) { float[][] rng = (minmax == null) ? null : ((float[][]) minmax - .get(features[i].getType())); + .get(feature.getType())); if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) { - tooltipText2.append(" Score=" + features[i].getScore()); + tooltipText2.append(" Score=" + feature.getScore()); } } - if (features[i].getValue("status") != null) + if (feature.getValue("status") != null) { - String status = features[i].getValue("status").toString(); + String status = feature.getValue("status").toString(); if (status.length() > 0) { - tooltipText2.append("; (" + features[i].getValue("status") + tooltipText2.append("; (" + feature.getValue("status") + ")"); } } } } - if (features[i].links != null) + if (feature.links != null) { if (linkImageURL != null) { @@ -178,7 +179,7 @@ public class SequenceAnnotationReport } else { - for (String urlstring : (Vector) features[i].links) + for (String urlstring : (Vector) feature.links) { try { @@ -364,7 +365,6 @@ public class SequenceAnnotationReport // ADD NON POSITIONAL SEQUENCE INFO SequenceFeature[] features = ds.getSequenceFeatures(); - SequenceFeature[] tfeat = new SequenceFeature[1]; if (showNpFeats && features != null) { for (int i = 0; i < features.length; i++) @@ -372,7 +372,8 @@ public class SequenceAnnotationReport if (features[i].begin == 0 && features[i].end == 0) { int sz = -tip.length(); - tfeat[0] = features[i]; + List tfeat = new ArrayList(); + tfeat.add(features[i]); appendFeatures(tip, 0, tfeat, minmax); sz += tip.length(); maxWidth = Math.max(maxWidth, sz); diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index 96c462c..3b9fb00 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -1027,13 +1027,21 @@ public class StockholmFile extends AlignFile } else { - label = (key = type2id(aa.label.toLowerCase())) + "_cons"; + key = type2id(aa.label.toLowerCase()); + if (key == null) + { + label = aa.label; + } + else + { + label = key + "_cons"; + } } - if (label == null) { label = aa.label; } + label = label.replace(" ", "_"); out.append(new Format("%-" + maxid + "s").form("#=GC " + label + " ")); @@ -1067,7 +1075,7 @@ public class StockholmFile extends AlignFile String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character .toString(sequenceI.getCharAt(k))) : annot.displayCharacter; - if (key.equals("SS")) + if (key != null && key.equals("SS")) { if (annot == null) { diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java index 465a672..2ecaf6c 100644 --- a/src/jalview/javascript/MouseOverStructureListener.java +++ b/src/jalview/javascript/MouseOverStructureListener.java @@ -202,7 +202,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source) .getSequenceRenderer(); FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av - .getShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer( + .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer( ((jalview.appletgui.AlignmentPanel) source).av) : null; if (fr != null) { diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 387bb7f..4bf8176 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -214,6 +214,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem createPNG = new JMenuItem(); + JMenuItem createBioJS = new JMenuItem(); + JMenuItem createSVG = new JMenuItem(); protected JMenuItem font = new JMenuItem(); @@ -1197,6 +1199,19 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem_actionPerformed(e); } }); + + // TODO uncomment when supported by MassageManager + // createBioJS.setText(MessageManager.getString("label.biojs_html_export")); + createBioJS.setText("BioJS"); + createBioJS.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + bioJSMenuItem_actionPerformed(e); + } + }); + overviewMenuItem.setText(MessageManager .getString("label.overview_window")); overviewMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -1603,7 +1618,6 @@ public class GAlignFrame extends JInternalFrame font_actionPerformed(e); } }); - seqLimits.setText(MessageManager .getString("label.show_sequence_limits")); seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); @@ -2353,6 +2367,7 @@ public class GAlignFrame extends JInternalFrame jMenu2.add(htmlMenuItem); jMenu2.add(epsFile); jMenu2.add(createPNG); + jMenu2.add(createBioJS); jMenu2.add(createSVG); addSequenceMenu.add(addFromFile); addSequenceMenu.add(addFromText); @@ -2611,6 +2626,11 @@ public class GAlignFrame extends JInternalFrame { } + protected void bioJSMenuItem_actionPerformed(ActionEvent e) + { + + } + protected void closeMenuItem_actionPerformed(boolean b) { } diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java index 4751d25..97ec9fe 100755 --- a/src/jalview/jbgui/GDesktop.java +++ b/src/jalview/jbgui/GDesktop.java @@ -22,10 +22,16 @@ package jalview.jbgui; import jalview.util.MessageManager; -import java.awt.*; -import java.awt.event.*; +import java.awt.FlowLayout; +import java.awt.Toolkit; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; -import javax.swing.*; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JFrame; +import javax.swing.JMenu; +import javax.swing.JMenuBar; +import javax.swing.JMenuItem; /** * DOCUMENT ME! @@ -374,7 +380,7 @@ public class GDesktop extends JFrame toolsMenu.add(showConsole); toolsMenu.add(showNews); toolsMenu.add(garbageCollect); - toolsMenu.add(snapShotWindow); + // toolsMenu.add(snapShotWindow); inputMenu.add(inputLocalFileMenuItem); inputMenu.add(inputURLMenuItem); inputMenu.add(inputTextboxMenuItem); diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 5569c24..610f32e 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -782,6 +782,15 @@ public class GPreferences extends JPanel structViewer.setBounds(new Rectangle(160, ypos, 120, height)); structViewer.addItem(Viewer.JMOL.name()); structViewer.addItem(Viewer.CHIMERA.name()); + structViewer.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + structureViewer_actionPerformed((String) structViewer + .getSelectedItem()); + } + }); structureTab.add(structViewer); ypos += lineSpacing; @@ -819,6 +828,15 @@ public class GPreferences extends JPanel } /** + * Action on choosing a structure viewer from combobox options. + * + * @param selectedItem + */ + protected void structureViewer_actionPerformed(String selectedItem) + { + } + + /** * Show a dialog for the user to choose a file. Returns the chosen path, or * null on Cancel. * diff --git a/src/jalview/json/binding/v1/BioJsAlignmentPojo.java b/src/jalview/json/binding/v1/BioJsAlignmentPojo.java new file mode 100644 index 0000000..8e8747f --- /dev/null +++ b/src/jalview/json/binding/v1/BioJsAlignmentPojo.java @@ -0,0 +1,151 @@ +package jalview.json.binding.v1; + +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.RNAInteractionColourScheme; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.ZappoColourScheme; + +import java.util.ArrayList; + +public class BioJsAlignmentPojo +{ + private String globalColorScheme = "none"; + + private String jalviewVersion; + + private String webStartUrl; + private ArrayList seqs = new ArrayList(); + + public BioJsAlignmentPojo() + { + + } + public ArrayList getSeqs() + { + return seqs; + } + + public void setSeqs(ArrayList seqs) + { + this.seqs = seqs; + } + public String getGlobalColorScheme() + { + return globalColorScheme; + } + public void setGlobalColorScheme(String globalColorScheme) + { + for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper + .values()) + { + if (cs.getJalviewName().equals(globalColorScheme)) + { + this.globalColorScheme = cs.getBioJsName(); + break; + } + } + + // JALVIEW colors not in biojs + // Blosum62 + // T-Coffee Scores (almost same with Blosom62 + // RNA Interaction type - no color applied + // RNA Helices - missing + + // BIOJS Colour not in jalview + // schemes.push name: "Lesk", id: "lesk" + // schemes.push name: "Cinema", id: "cinema" + // schemes.push name: "MAE", id: "mae" + // schemes.push name: "Clustal2", id: "clustal2" + + } + + + public String getJalviewVersion() + { + return jalviewVersion; + } + + public void setJalviewVersion(String jalviewVersion) + { + this.jalviewVersion = jalviewVersion; + } + + public String getWebStartUrl() + { + return webStartUrl; + } + + public void setWebStartUrl(String webStartUrl) + { + this.webStartUrl = webStartUrl; + } + + public enum JalviewBioJsColorSchemeMapper + { + USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo", + null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo", + "zappo", new ZappoColourScheme()), TAYLOR( + "Taylor", "taylor", new TaylorColourScheme()), NUCLEOTIDE( + "Nucleotide", "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE( + "Purine/Pyrimidine", "purine", + new PurinePyrimidineColourScheme()), HELIX_PROPENCITY( + "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY( + "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY( + "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX( + "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC( + "Hydrophobic", "hydro", new HydrophobicColourScheme()), + + // The color types below are not yet supported by BioJs MSA viewer + T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", + null), RNA_INT_TYPE( + "RNA Interaction type", "RNA Interaction type", + new RNAInteractionColourScheme()), BLOSUM62("Blosum62", + "Blosum62", new Blosum62ColourScheme()), RNA_HELICES( + "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY( + "% Identity", "pid", + new PIDColourScheme()); + + private String jalviewName; + private String bioJsName; + + private ColourSchemeI jvColourScheme; + + private JalviewBioJsColorSchemeMapper(String jalviewName, + String bioJsName, ColourSchemeI jvColourScheme) + { + this.jalviewName = jalviewName; + this.bioJsName = bioJsName; + this.setJvColourScheme(jvColourScheme); + } + + public String getJalviewName() + { + return jalviewName; + } + + public String getBioJsName() + { + return bioJsName; + } + + public ColourSchemeI getJvColourScheme() + { + return jvColourScheme; + } + + public void setJvColourScheme(ColourSchemeI jvColourScheme) + { + this.jvColourScheme = jvColourScheme; + } + + } +} diff --git a/src/jalview/json/binding/v1/BioJsFeaturePojo.java b/src/jalview/json/binding/v1/BioJsFeaturePojo.java new file mode 100644 index 0000000..3c2fdda --- /dev/null +++ b/src/jalview/json/binding/v1/BioJsFeaturePojo.java @@ -0,0 +1,60 @@ +package jalview.json.binding.v1; + +public class BioJsFeaturePojo +{ + + private int xstart; + + private int xend; + + private String text; + + private String fillColor; + + public BioJsFeaturePojo() + { + } + + + public String getText() + { + return text; + } + + public void setText(String text) + { + this.text = text; + } + + public String getFillColor() + { + return "#" + fillColor; + } + + public void setFillColor(String fillColor) + { + this.fillColor = fillColor; + } + + public int getXstart() + { + return xstart; + } + + public void setXstart(int xstart) + { + this.xstart = xstart; + } + + public int getXend() + { + return xend; + } + + public void setXend(int xend) + { + this.xend = xend; + } + + +} diff --git a/src/jalview/json/binding/v1/BioJsSeqPojo.java b/src/jalview/json/binding/v1/BioJsSeqPojo.java new file mode 100644 index 0000000..bac8601 --- /dev/null +++ b/src/jalview/json/binding/v1/BioJsSeqPojo.java @@ -0,0 +1,90 @@ +package jalview.json.binding.v1; + +import java.util.ArrayList; + + +public class BioJsSeqPojo +{ + private String seq; + + private String name; + + private String id; + + private int start; + + private int end; + + private ArrayList features = new ArrayList(); + + public BioJsSeqPojo() + { + } + + public BioJsSeqPojo(int start, int end, String id, String name, String seq) + { + this.id = id; + this.name = name; + this.seq = seq; + } + public String getSeq() + { + return seq; + } + + public void setSeq(String seq) + { + this.seq = seq; + } + + public String getName() + { + + return name; + } + + public void setName(String name) + { + this.name = name; + } + + public String getId() + { + return id; + } + + public void setId(String id) + { + this.id = id; + } + + public int getStart() + { + return start; + } + + public void setStart(int start) + { + this.start = start; + } + + public int getEnd() + { + return end; + } + + public void setEnd(int end) + { + this.end = end; + } + + public ArrayList getFeatures() + { + return features; + } + + public void setFeatures(ArrayList features) + { + this.features = features; + } +} diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java new file mode 100644 index 0000000..5e6ac29 --- /dev/null +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -0,0 +1,435 @@ +package jalview.renderer.seqfeatures; + +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; + +import java.awt.AlphaComposite; +import java.awt.Color; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.image.BufferedImage; + +public class FeatureRenderer extends + jalview.viewmodel.seqfeatures.FeatureRendererModel +{ + + FontMetrics fm; + + int charOffset; + + boolean offscreenRender = false; + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + * @param seq + * DOCUMENT ME! + * @param sg + * DOCUMENT ME! + * @param start + * DOCUMENT ME! + * @param end + * DOCUMENT ME! + * @param x1 + * DOCUMENT ME! + * @param y1 + * DOCUMENT ME! + * @param width + * DOCUMENT ME! + * @param height + * DOCUMENT ME! + */ + protected SequenceI lastSeq; + + char s; + + int i; + + int av_charHeight, av_charWidth; + + boolean av_validCharWidth, av_isShowSeqFeatureHeight; + + protected void updateAvConfig() + { + av_charHeight = av.getCharHeight(); + av_charWidth = av.getCharWidth(); + av_validCharWidth = av.isValidCharWidth(); + av_isShowSeqFeatureHeight = av.isShowSequenceFeaturesHeight(); + } + + void renderFeature(Graphics g, SequenceI seq, int fstart, int fend, + Color featureColour, int start, int end, int y1) + { + updateAvConfig(); + if (((fstart <= end) && (fend >= start))) + { + if (fstart < start) + { // fix for if the feature we have starts before the sequence start, + fstart = start; // but the feature end is still valid!! + } + + if (fend >= end) + { + fend = end; + } + int pady = (y1 + av_charHeight) - av_charHeight / 5; + for (i = fstart; i <= fend; i++) + { + s = seq.getCharAt(i); + + if (jalview.util.Comparison.isGap(s)) + { + continue; + } + + g.setColor(featureColour); + + g.fillRect((i - start) * av_charWidth, y1, av_charWidth, + av_charHeight); + + if (offscreenRender || !av_validCharWidth) + { + continue; + } + + g.setColor(Color.white); + charOffset = (av_charWidth - fm.charWidth(s)) / 2; + g.drawString(String.valueOf(s), charOffset + + (av_charWidth * (i - start)), pady); + + } + } + } + + void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend, + Color featureColour, int start, int end, int y1, byte[] bs) + { + updateAvConfig(); + if (((fstart <= end) && (fend >= start))) + { + if (fstart < start) + { // fix for if the feature we have starts before the sequence start, + fstart = start; // but the feature end is still valid!! + } + + if (fend >= end) + { + fend = end; + } + int pady = (y1 + av_charHeight) - av_charHeight / 5; + int ystrt = 0, yend = av_charHeight; + if (bs[0] != 0) + { + // signed - zero is always middle of residue line. + if (bs[1] < 128) + { + yend = av_charHeight * (128 - bs[1]) / 512; + ystrt = av_charHeight - yend / 2; + } + else + { + ystrt = av_charHeight / 2; + yend = av_charHeight * (bs[1] - 128) / 512; + } + } + else + { + yend = av_charHeight * bs[1] / 255; + ystrt = av_charHeight - yend; + + } + for (i = fstart; i <= fend; i++) + { + s = seq.getCharAt(i); + + if (jalview.util.Comparison.isGap(s)) + { + continue; + } + + g.setColor(featureColour); + int x = (i - start) * av_charWidth; + g.drawRect(x, y1, av_charWidth, av_charHeight); + g.fillRect(x, y1 + ystrt, av_charWidth, yend); + + if (offscreenRender || !av_validCharWidth) + { + continue; + } + + g.setColor(Color.black); + charOffset = (av_charWidth - fm.charWidth(s)) / 2; + g.drawString(String.valueOf(s), charOffset + + (av_charWidth * (i - start)), pady); + + } + } + } + + BufferedImage offscreenImage; + + public Color findFeatureColour(Color initialCol, SequenceI seq, int res) + { + return new Color(findFeatureColour(initialCol.getRGB(), seq, res)); + } + + /** + * This is used by the Molecule Viewer and Overview to get the accurate + * colourof the rendered sequence + */ + public synchronized int findFeatureColour(int initialCol, final SequenceI seq, + int column) + { + if (!av.isShowSequenceFeatures()) + { + return initialCol; + } + + final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq + .getDatasetSequence() : seq; + if (seq != lastSeq) + { + lastSeq = seq; + sequenceFeatures = aseq.getSequenceFeatures(); + if (sequenceFeatures != null) + { + sfSize = sequenceFeatures.length; + } + } + else + { + if (sequenceFeatures != aseq.getSequenceFeatures()) + { + sequenceFeatures = aseq.getSequenceFeatures(); + if (sequenceFeatures != null) + { + sfSize = sequenceFeatures.length; + } + } + } + + if (sequenceFeatures == null || sfSize == 0) + { + return initialCol; + } + + if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column))) + { + return Color.white.getRGB(); + } + + // Only bother making an offscreen image if transparency is applied + if (transparency != 1.0f && offscreenImage == null) + { + offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB); + } + + currentColour = null; + // TODO: non-threadsafe - each rendering thread needs its own instance of + // the feature renderer - or this should be synchronized. + offscreenRender = true; + + if (offscreenImage != null) + { + offscreenImage.setRGB(0, 0, initialCol); + drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0); + + return offscreenImage.getRGB(0, 0); + } + else + { + drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1); + + if (currentColour == null) + { + return initialCol; + } + else + { + return ((Integer) currentColour).intValue(); + } + } + + } + + private volatile SequenceFeature[] sequenceFeatures; + + int sfSize; + + int sfindex; + + int spos; + + int epos; + + public synchronized void drawSequence(Graphics g, final SequenceI seq, + int start, int end, int y1) + { + final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq + .getDatasetSequence() : seq; + if (aseq.getSequenceFeatures() == null + || aseq.getSequenceFeatures().length == 0) + { + return; + } + + if (g != null) + { + fm = g.getFontMetrics(); + } + + updateFeatures(); + + if (lastSeq == null || seq != lastSeq + || aseq.getSequenceFeatures() != sequenceFeatures) + { + lastSeq = seq; + sequenceFeatures = aseq.getSequenceFeatures(); + } + + if (transparency != 1 && g != null) + { + Graphics2D g2 = (Graphics2D) g; + g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + transparency)); + } + + if (!offscreenRender) + { + spos = lastSeq.findPosition(start); + epos = lastSeq.findPosition(end); + } + + sfSize = sequenceFeatures.length; + String type; + for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) + { + type = renderOrder[renderIndex]; + + if (type == null || !showFeatureOfType(type)) + { + continue; + } + + // loop through all features in sequence to find + // current feature to render + for (sfindex = 0; sfindex < sfSize; sfindex++) + { + if (!sequenceFeatures[sfindex].type.equals(type)) + { + continue; + } + + if (featureGroups != null + && sequenceFeatures[sfindex].featureGroup != null + && sequenceFeatures[sfindex].featureGroup.length() != 0 + && featureGroups + .containsKey(sequenceFeatures[sfindex].featureGroup) + && !featureGroups + .get(sequenceFeatures[sfindex].featureGroup) + .booleanValue()) + { + continue; + } + + if (!offscreenRender + && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex] + .getEnd() < spos)) + { + continue; + } + + if (offscreenRender && offscreenImage == null) + { + if (sequenceFeatures[sfindex].begin <= start + && sequenceFeatures[sfindex].end >= start) + { + // this is passed out to the overview and other sequence renderers + // (e.g. molecule viewer) to get displayed colour for rendered + // sequence + currentColour = new Integer( + getColour(sequenceFeatures[sfindex]).getRGB()); + // used to be retreived from av.featuresDisplayed + // currentColour = av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type); + + } + } + else if (sequenceFeatures[sfindex].type.equals("disulfide bond")) + { + + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + getColour(sequenceFeatures[sfindex]) + // new Color(((Integer) av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type)).intValue()) + , start, end, y1); + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex]) + // new Color(((Integer) av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type)).intValue()) + , start, end, y1); + + } + else if (showFeature(sequenceFeatures[sfindex])) + { + if (av_isShowSeqFeatureHeight + && sequenceFeatures[sfindex].score != Float.NaN) + { + renderScoreFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex]), start, end, y1, + normaliseScore(sequenceFeatures[sfindex])); + } + else + { + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex]), start, end, y1); + } + } + + } + + } + + if (transparency != 1.0f && g != null && transparencyAvailable) + { + Graphics2D g2 = (Graphics2D) g; + g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + 1.0f)); + } + } + + boolean transparencyAvailable = true; + + protected void setTransparencyAvailable(boolean isTransparencyAvailable) + { + transparencyAvailable = isTransparencyAvailable; + } + + @Override + public boolean isTransparencyAvailable() + { + return transparencyAvailable; + } + + /** + * Called when alignment in associated view has new/modified features to + * discover and display. + * + */ + public void featuresAdded() + { + lastSeq = null; + findAllFeatures(); + } +} diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index 3cada8b..85ec3aec0 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -258,7 +258,7 @@ public class AnnotationColourGradient extends FollowerColourScheme public Color findColour(char c, int j, SequenceI seq) { Color currentColour = Color.white; - AlignmentAnnotation annotation = (seqAssociated ? seqannot.get(seq) + AlignmentAnnotation annotation = (seqAssociated && seqannot!=null ? seqannot.get(seq) : this.annotation); if (annotation == null) { @@ -286,7 +286,8 @@ public class AnnotationColourGradient extends FollowerColourScheme || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value : aj.value <= annotationThreshold.value))) { - if (predefinedColours && aj.colour != null) + if (predefinedColours && aj.colour != null + && !aj.colour.equals(Color.black)) { currentColour = aj.colour; } diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java index 41f7781..70c7685 100755 --- a/src/jalview/schemes/Blosum62ColourScheme.java +++ b/src/jalview/schemes/Blosum62ColourScheme.java @@ -21,14 +21,13 @@ package jalview.schemes; import jalview.analysis.AAFrequency; - -import java.awt.Color; -import java.util.Map; - import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceI; +import java.awt.Color; +import java.util.Map; + public class Blosum62ColourScheme extends ResidueColourScheme { public Blosum62ColourScheme() @@ -59,6 +58,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme if (max.indexOf(res) > -1) { + // TODO use a constant here? currentColour = new Color(154, 154, 255); } else @@ -74,6 +74,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme if (c > 0) { + // TODO use a constant here? currentColour = new Color(204, 204, 255); } else diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index 8acf1f2..d13f0a9 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -20,6 +20,7 @@ */ package jalview.schemes; +import jalview.analysis.scoremodels.FeatureScoreModel; import jalview.analysis.scoremodels.PIDScoreModel; import jalview.api.analysis.ScoreModelI; @@ -1498,6 +1499,7 @@ public class ResidueProperties // scoreMatrices.put("Conservation EnhPos", new // ScoreMatrix("Conservation EnhPos",propMatrixEpos,0)); scoreMatrices.put("PID", new PIDScoreModel()); + scoreMatrices.put("Displayed Features", new FeatureScoreModel()); } private ResidueProperties() diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 4359879..af00798 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -522,7 +522,6 @@ public class StructureSelectionManager { return; } - boolean removeMapping = true; String[] handlepdbs; Vector pdbs = new Vector(); for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++])) diff --git a/src/jalview/util/ColorUtils.java b/src/jalview/util/ColorUtils.java index fd76086..44ce010 100644 --- a/src/jalview/util/ColorUtils.java +++ b/src/jalview/util/ColorUtils.java @@ -60,6 +60,26 @@ public class ColorUtils } /** + * Convert to Tk colour code format + * + * @param colour + * @return + * @see http + * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/colortool.html# + * tkcode + */ + public static final String toTkCode(Color colour) + { + String colstring = "#" + ((colour.getRed() < 16) ? "0" : "") + + Integer.toHexString(colour.getRed()) + + ((colour.getGreen() < 16) ? "0" : "") + + Integer.toHexString(colour.getGreen()) + + ((colour.getBlue() < 16) ? "0" : "") + + Integer.toHexString(colour.getBlue()); + return colstring; + } + + /** * Returns a colour three shades darker. Note you can't guarantee that * brighterThan reverses this, as darkerThan may result in black. * diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 1b42faf..a2da591 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -24,6 +24,7 @@ import jalview.analysis.Conservation; import jalview.api.AlignCalcManagerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.FeaturesDisplayedI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; @@ -696,6 +697,7 @@ public abstract class AlignmentViewport implements AlignViewportI sequenceSetID = new String(newid); } + @Override public String getSequenceSetId() { if (sequenceSetID == null) @@ -1659,4 +1661,97 @@ public abstract class AlignmentViewport implements AlignViewportI { sequenceColours = null; }; + + FeaturesDisplayedI featuresDisplayed = null; + + @Override + public FeaturesDisplayedI getFeaturesDisplayed() + { + return featuresDisplayed; + } + + public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI) + { + featuresDisplayed = featuresDisplayedI; + } + + public boolean areFeaturesDisplayed() + { + return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0; + } + + /** + * display setting for showing/hiding sequence features on alignment view + */ + boolean showSequenceFeatures = false; + + /** + * set the flag + * + * @param b + * features are displayed if true + */ + @Override + public void setShowSequenceFeatures(boolean b) + { + showSequenceFeatures = b; + } + @Override + public boolean isShowSequenceFeatures() + { + return showSequenceFeatures; + } + + boolean showSeqFeaturesHeight; + + public void setShowSequenceFeaturesHeight(boolean selected) + { + showSeqFeaturesHeight = selected; + } + + public boolean isShowSequenceFeaturesHeight() + { + return showSeqFeaturesHeight; + } + + private boolean showAnnotation = true; + + private boolean rightAlignIds = false; + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowAnnotation() + { + return isShowAnnotation(); + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setShowAnnotation(boolean b) + { + showAnnotation = b; + } + + public boolean isShowAnnotation() + { + return showAnnotation; + } + + public boolean isRightAlignIds() + { + return rightAlignIds; + } + + public void setRightAlignIds(boolean rightAlignIds) + { + this.rightAlignIds = rightAlignIds; + } + } diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java new file mode 100644 index 0000000..c7cee04 --- /dev/null +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -0,0 +1,949 @@ +package jalview.viewmodel.seqfeatures; + +import jalview.api.AlignViewportI; +import jalview.api.FeaturesDisplayedI; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.renderer.seqfeatures.FeatureRenderer; +import jalview.schemes.GraduatedColor; +import jalview.viewmodel.AlignmentViewport; + +import java.awt.Color; +import java.beans.PropertyChangeListener; +import java.beans.PropertyChangeSupport; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.concurrent.ConcurrentHashMap; + +public abstract class FeatureRendererModel implements + jalview.api.FeatureRenderer +{ + + /** + * global transparency for feature + */ + protected float transparency = 1.0f; + + protected Map featureColours = new ConcurrentHashMap(); + + protected Map featureGroups = new ConcurrentHashMap(); + + protected Object currentColour; + + protected String[] renderOrder; + + protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( + this); + + protected AlignmentViewport av; + + public AlignViewportI getViewport() + { + return av; + } + + public FeatureRendererSettings getSettings() + { + return new FeatureRendererSettings(this); + } + + public void transferSettings(FeatureRendererSettings fr) + { + this.renderOrder = fr.renderOrder; + this.featureGroups = fr.featureGroups; + this.featureColours = fr.featureColours; + this.transparency = fr.transparency; + this.featureOrder = fr.featureOrder; + } + + /** + * update from another feature renderer + * + * @param fr + * settings to copy + */ + public void transferSettings(jalview.api.FeatureRenderer _fr) + { + FeatureRenderer fr = (FeatureRenderer) _fr; + FeatureRendererSettings frs = new FeatureRendererSettings(fr); + this.renderOrder = frs.renderOrder; + this.featureGroups = frs.featureGroups; + this.featureColours = frs.featureColours; + this.transparency = frs.transparency; + this.featureOrder = frs.featureOrder; + if (av != null && av != fr.getViewport()) + { + // copy over the displayed feature settings + if (_fr.getFeaturesDisplayed() != null) + { + FeaturesDisplayedI fd = getFeaturesDisplayed(); + if (fd == null) + { + setFeaturesDisplayedFrom(_fr.getFeaturesDisplayed()); + } + else + { + synchronized (fd) + { + fd.clear(); + java.util.Iterator fdisp = _fr.getFeaturesDisplayed() + .getVisibleFeatures(); + while (fdisp.hasNext()) + { + fd.setVisible(fdisp.next()); + } + } + } + } + } + } + + public void setFeaturesDisplayedFrom(FeaturesDisplayedI featuresDisplayed) + { + av.setFeaturesDisplayed(new FeaturesDisplayed(featuresDisplayed)); + } + + @Override + public void setVisible(String featureType) + { + FeaturesDisplayedI fdi = av.getFeaturesDisplayed(); + if (fdi == null) + { + av.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); + } + if (!fdi.isRegistered(featureType)) + { + pushFeatureType(Arrays.asList(new String[] + { featureType })); + } + fdi.setVisible(featureType); + } + + @Override + public void setAllVisible(List featureTypes) + { + FeaturesDisplayedI fdi = av.getFeaturesDisplayed(); + if (fdi == null) + { + av.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); + } + List nft = new ArrayList(); + for (String featureType : featureTypes) + { + if (!fdi.isRegistered(featureType)) + { + nft.add(featureType); + } + } + if (nft.size() > 0) + { + pushFeatureType(nft); + } + fdi.setAllVisible(featureTypes); + } + + /** + * push a set of new types onto the render order stack. Note - this is a + * direct mechanism rather than the one employed in updateRenderOrder + * + * @param types + */ + private void pushFeatureType(List types) + { + + int ts = types.size(); + String neworder[] = new String[(renderOrder == null ? 0 + : renderOrder.length) + ts]; + types.toArray(neworder); + if (renderOrder != null) + { + System.arraycopy(neworder,0,neworder,renderOrder.length,ts); + System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length); + } + renderOrder = neworder; + } + + protected Hashtable minmax = new Hashtable(); + + public Hashtable getMinMax() + { + return minmax; + } + + /** + * normalise a score against the max/min bounds for the feature type. + * + * @param sequenceFeature + * @return byte[] { signed, normalised signed (-127 to 127) or unsigned + * (0-255) value. + */ + protected final byte[] normaliseScore(SequenceFeature sequenceFeature) + { + float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0]; + final byte[] r = new byte[] + { 0, (byte) 255 }; + if (mm != null) + { + if (r[0] != 0 || mm[0] < 0.0) + { + r[0] = 1; + r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1])); + } + else + { + r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1])); + } + } + return r; + } + + boolean newFeatureAdded = false; + + boolean findingFeatures = false; + + protected boolean updateFeatures() + { + if (av.getFeaturesDisplayed() == null || renderOrder == null + || newFeatureAdded) + { + findAllFeatures(); + if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1) + { + return false; + } + } + // TODO: decide if we should check for the visible feature count first + return true; + } + + /** + * search the alignment for all new features, give them a colour and display + * them. Then fires a PropertyChangeEvent on the changeSupport object. + * + */ + protected void findAllFeatures() + { + synchronized (firing) + { + if (firing.equals(Boolean.FALSE)) + { + firing = Boolean.TRUE; + findAllFeatures(true); // add all new features as visible + changeSupport.firePropertyChange("changeSupport", null, null); + firing = Boolean.FALSE; + } + } + } + + @Override + public List findFeaturesAtRes(SequenceI sequence, int res) + { + ArrayList tmp = new ArrayList(); + SequenceFeature[] features = sequence.getSequenceFeatures(); + + while (features == null && sequence.getDatasetSequence() != null) + { + sequence = sequence.getDatasetSequence(); + features = sequence.getSequenceFeatures(); + } + + if (features != null) + { + for (int i = 0; i < features.length; i++) + { + if (!av.areFeaturesDisplayed() + || !av.getFeaturesDisplayed().isVisible( + features[i].getType())) + { + continue; + } + + if (features[i].featureGroup != null + && featureGroups != null + && featureGroups.containsKey(features[i].featureGroup) + && !featureGroups.get(features[i].featureGroup) + .booleanValue()) + { + continue; + } + + if ((features[i].getBegin() <= res) + && (features[i].getEnd() >= res)) + { + tmp.add(features[i]); + } + } + } + return tmp; + } + + /** + * Searches alignment for all features and updates colours + * + * @param newMadeVisible + * if true newly added feature types will be rendered immediatly + * TODO: check to see if this method should actually be proxied so + * repaint events can be propagated by the renderer code + */ + @Override + public synchronized void findAllFeatures(boolean newMadeVisible) + { + newFeatureAdded = false; + + if (findingFeatures) + { + newFeatureAdded = true; + return; + } + + findingFeatures = true; + if (av.getFeaturesDisplayed() == null) + { + av.setFeaturesDisplayed(new FeaturesDisplayed()); + } + FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed(); + + ArrayList allfeatures = new ArrayList(); + ArrayList oldfeatures = new ArrayList(); + if (renderOrder != null) + { + for (int i = 0; i < renderOrder.length; i++) + { + if (renderOrder[i] != null) + { + oldfeatures.add(renderOrder[i]); + } + } + } + if (minmax == null) + { + minmax = new Hashtable(); + } + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) + { + SequenceI asq = alignment.getSequenceAt(i); + SequenceI dasq = asq.getDatasetSequence(); + SequenceFeature[] features = dasq != null ? dasq + .getSequenceFeatures() : asq.getSequenceFeatures(); + + if (features == null) + { + continue; + } + + int index = 0; + while (index < features.length) + { + if (!featuresDisplayed.isRegistered(features[index].getType())) + { + String fgrp = features[index].getFeatureGroup(); + if (fgrp != null) + { + Boolean groupDisplayed = featureGroups.get(fgrp); + if (groupDisplayed == null) + { + groupDisplayed = Boolean.valueOf(newMadeVisible); + featureGroups.put(fgrp, groupDisplayed); + } + if (!groupDisplayed.booleanValue()) + { + index++; + continue; + } + } + if (!(features[index].begin == 0 && features[index].end == 0)) + { + // If beginning and end are 0, the feature is for the whole sequence + // and we don't want to render the feature in the normal way + + if (newMadeVisible + && !oldfeatures.contains(features[index].getType())) + { + // this is a new feature type on the alignment. Mark it for + // display. + featuresDisplayed.setVisible(features[index].getType()); + setOrder(features[index].getType(), 0); + } + } + } + if (!allfeatures.contains(features[index].getType())) + { + allfeatures.add(features[index].getType()); + } + if (features[index].score != Float.NaN) + { + int nonpos = features[index].getBegin() >= 1 ? 0 : 1; + float[][] mm = (float[][]) minmax.get(features[index].getType()); + if (mm == null) + { + mm = new float[][] + { null, null }; + minmax.put(features[index].getType(), mm); + } + if (mm[nonpos] == null) + { + mm[nonpos] = new float[] + { features[index].score, features[index].score }; + + } + else + { + if (mm[nonpos][0] > features[index].score) + { + mm[nonpos][0] = features[index].score; + } + if (mm[nonpos][1] < features[index].score) + { + mm[nonpos][1] = features[index].score; + } + } + } + index++; + } + } + updateRenderOrder(allfeatures); + findingFeatures = false; + } + + protected Boolean firing = Boolean.FALSE; + + /** + * replaces the current renderOrder with the unordered features in + * allfeatures. The ordering of any types in both renderOrder and allfeatures + * is preserved, and all new feature types are rendered on top of the existing + * types, in the order given by getOrder or the order given in allFeatures. + * Note. this operates directly on the featureOrder hash for efficiency. TODO: + * eliminate the float storage for computing/recalling the persistent ordering + * New Cability: updates min/max for colourscheme range if its dynamic + * + * @param allFeatures + */ + private void updateRenderOrder(List allFeatures) + { + List allfeatures = new ArrayList(allFeatures); + String[] oldRender = renderOrder; + renderOrder = new String[allfeatures.size()]; + Object mmrange, fc = null; + boolean initOrders = (featureOrder == null); + int opos = 0; + if (oldRender != null && oldRender.length > 0) + { + for (int j = 0; j < oldRender.length; j++) + { + if (oldRender[j] != null) + { + if (initOrders) + { + setOrder(oldRender[j], (1 - (1 + (float) j) + / oldRender.length)); + } + if (allfeatures.contains(oldRender[j])) + { + renderOrder[opos++] = oldRender[j]; // existing features always + // appear below new features + allfeatures.remove(oldRender[j]); + if (minmax != null) + { + mmrange = minmax.get(oldRender[j]); + if (mmrange != null) + { + fc = featureColours.get(oldRender[j]); + if (fc != null && fc instanceof GraduatedColor + && ((GraduatedColor) fc).isAutoScale()) + { + ((GraduatedColor) fc).updateBounds( + ((float[][]) mmrange)[0][0], + ((float[][]) mmrange)[0][1]); + } + } + } + } + } + } + } + if (allfeatures.size() == 0) + { + // no new features - leave order unchanged. + return; + } + int i = allfeatures.size() - 1; + int iSize = i; + boolean sort = false; + String[] newf = new String[allfeatures.size()]; + float[] sortOrder = new float[allfeatures.size()]; + for (String newfeat : allfeatures) + { + newf[i] = newfeat; + if (minmax != null) + { + // update from new features minmax if necessary + mmrange = minmax.get(newf[i]); + if (mmrange != null) + { + fc = featureColours.get(newf[i]); + if (fc != null && fc instanceof GraduatedColor + && ((GraduatedColor) fc).isAutoScale()) + { + ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0], + ((float[][]) mmrange)[0][1]); + } + } + } + if (initOrders || !featureOrder.containsKey(newf[i])) + { + int denom = initOrders ? allfeatures.size() : featureOrder.size(); + // new unordered feature - compute persistent ordering at head of + // existing features. + setOrder(newf[i], i / (float) denom); + } + // set order from newly found feature from persisted ordering. + sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue(); + if (i < iSize) + { + // only sort if we need to + sort = sort || sortOrder[i] > sortOrder[i + 1]; + } + i--; + } + if (iSize > 1 && sort) + { + jalview.util.QuickSort.sort(sortOrder, newf); + } + sortOrder = null; + System.arraycopy(newf, 0, renderOrder, opos, newf.length); + } + + /** + * get a feature style object for the given type string. Creates a + * java.awt.Color for a featureType with no existing colourscheme. TODO: + * replace return type with object implementing standard abstract colour/style + * interface + * + * @param featureType + * @return java.awt.Color or GraduatedColor + */ + public Object getFeatureStyle(String featureType) + { + Object fc = featureColours.get(featureType); + if (fc == null) + { + jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); + Color col = ucs.createColourFromName(featureType); + featureColours.put(featureType, fc = col); + } + return fc; + } + + /** + * return a nominal colour for this feature + * + * @param featureType + * @return standard color, or maximum colour for graduated colourscheme + */ + public Color getColour(String featureType) + { + Object fc = getFeatureStyle(featureType); + + if (fc instanceof Color) + { + return (Color) fc; + } + else + { + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).getMaxColor(); + } + } + throw new Error("Implementation Error: Unrecognised render object " + + fc.getClass() + " for features of type " + featureType); + } + + /** + * calculate the render colour for a specific feature using current feature + * settings. + * + * @param feature + * @return render colour for the given feature + */ + public Color getColour(SequenceFeature feature) + { + Object fc = getFeatureStyle(feature.getType()); + if (fc instanceof Color) + { + return (Color) fc; + } + else + { + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).findColor(feature); + } + } + throw new Error("Implementation Error: Unrecognised render object " + + fc.getClass() + " for features of type " + feature.getType()); + } + + protected boolean showFeature(SequenceFeature sequenceFeature) + { + Object fc = getFeatureStyle(sequenceFeature.type); + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).isColored(sequenceFeature); + } + else + { + return true; + } + } + + protected boolean showFeatureOfType(String type) + { + return av.getFeaturesDisplayed().isVisible(type); + } + + public void setColour(String featureType, Object col) + { + // overwrite + // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof + // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null; + // Object c = featureColours.get(featureType); + // if (c == null || c instanceof Color || (c instanceof GraduatedColor && + // !((GraduatedColor)c).getMaxColor().equals(_col))) + { + featureColours.put(featureType, col); + } + } + + public void setTransparency(float value) + { + transparency = value; + } + + public float getTransparency() + { + return transparency; + } + + Map featureOrder = null; + + /** + * analogous to colour - store a normalized ordering for all feature types in + * this rendering context. + * + * @param type + * Feature type string + * @param position + * normalized priority - 0 means always appears on top, 1 means + * always last. + */ + public float setOrder(String type, float position) + { + if (featureOrder == null) + { + featureOrder = new Hashtable(); + } + featureOrder.put(type, new Float(position)); + return position; + } + + /** + * get the global priority (0 (top) to 1 (bottom)) + * + * @param type + * @return [0,1] or -1 for a type without a priority + */ + public float getOrder(String type) + { + if (featureOrder != null) + { + if (featureOrder.containsKey(type)) + { + return ((Float) featureOrder.get(type)).floatValue(); + } + } + return -1; + } + + @Override + public Map getFeatureColours() + { + return new ConcurrentHashMap(featureColours); + } + + /** + * Replace current ordering with new ordering + * + * @param data + * { String(Type), Colour(Type), Boolean(Displayed) } + */ + public void setFeaturePriority(Object[][] data) + { + setFeaturePriority(data, true); + } + + /** + * + * @param data + * { String(Type), Colour(Type), Boolean(Displayed) } + * @param visibleNew + * when true current featureDisplay list will be cleared + */ + public void setFeaturePriority(Object[][] data, boolean visibleNew) + { + FeaturesDisplayedI av_featuresdisplayed = null; + if (visibleNew) + { + if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null) + { + av.getFeaturesDisplayed().clear(); + } + else + { + av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed()); + } + } + else + { + av_featuresdisplayed = av.getFeaturesDisplayed(); + } + if (data == null) + { + return; + } + // The feature table will display high priority + // features at the top, but theses are the ones + // we need to render last, so invert the data + renderOrder = new String[data.length]; + + if (data.length > 0) + { + for (int i = 0; i < data.length; i++) + { + String type = data[i][0].toString(); + setColour(type, data[i][1]); // todo : typesafety - feature color + // interface object + if (((Boolean) data[i][2]).booleanValue()) + { + av_featuresdisplayed.setVisible(type); + } + + renderOrder[data.length - i - 1] = type; + } + } + + } + + /** + * @param listener + * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener) + */ + public void addPropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + /** + * @param listener + * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener) + */ + public void removePropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.removePropertyChangeListener(listener); + } + + public Set getAllFeatureColours() + { + return featureColours.keySet(); + } + + public void clearRenderOrder() + { + renderOrder = null; + } + + public boolean hasRenderOrder() + { + return renderOrder != null; + } + + public List getRenderOrder() + { + if (renderOrder == null) + { + return Arrays.asList(new String[] + {}); + } + return Arrays.asList(renderOrder); + } + + public int getFeatureGroupsSize() + { + return featureGroups != null ? 0 : featureGroups.size(); + } + + @Override + public List getFeatureGroups() + { + // conflict between applet and desktop - featureGroups returns the map in + // the desktop featureRenderer + return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays + .asList(featureGroups.keySet().toArray(new String[0])); + } + + public boolean checkGroupVisibility(String group, boolean newGroupsVisible) + { + if (featureGroups == null) + { + // then an exception happens next.. + } + if (featureGroups.containsKey(group)) + { + return featureGroups.get(group).booleanValue(); + } + if (newGroupsVisible) + { + featureGroups.put(group, new Boolean(true)); + return true; + } + return false; + } + + /** + * get visible or invisible groups + * + * @param visible + * true to return visible groups, false to return hidden ones. + * @return list of groups + */ + @Override + public List getGroups(boolean visible) + { + if (featureGroups != null) + { + ArrayList gp = new ArrayList(); + + for (Object grp : featureGroups.keySet()) + { + Boolean state = featureGroups.get(grp); + if (state.booleanValue() == visible) + { + gp.add(grp); + } + } + return gp; + } + return null; + } + + @Override + public void setGroupVisibility(String group, boolean visible) + { + featureGroups.put(group, new Boolean(visible)); + } + + @Override + public void setGroupVisibility(List toset, boolean visible) + { + if (toset != null && toset.size() > 0 && featureGroups != null) + { + boolean rdrw = false; + for (String gst : toset) + { + Boolean st = featureGroups.get(gst); + featureGroups.put(gst, new Boolean(visible)); + if (st != null) + { + rdrw = rdrw || (visible != st.booleanValue()); + } + } + if (rdrw) + { + // set local flag indicating redraw needed ? + } + } + } + + @Override + public Hashtable getDisplayedFeatureCols() + { + Hashtable fcols = new Hashtable(); + if (getViewport().getFeaturesDisplayed() == null) + { + return fcols; + } + Iterator en = getViewport().getFeaturesDisplayed() + .getVisibleFeatures(); + while (en.hasNext()) + { + String col = en.next(); + fcols.put(col, getColour(col)); + } + return fcols; + } + + @Override + public FeaturesDisplayedI getFeaturesDisplayed() + { + return av.getFeaturesDisplayed(); + } + + @Override + public String[] getDisplayedFeatureTypes() + { + String[] typ = null; + typ = getRenderOrder().toArray(new String[0]); + FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed(); + if (feature_disp != null) + { + synchronized (feature_disp) + { + for (int i = 0; i < typ.length; i++) + { + if (!feature_disp.isVisible(typ[i])) + { + typ[i] = null; + } + } + } + } + return typ; + } + + @Override + public String[] getDisplayedFeatureGroups() + { + String[] gps = null; + ArrayList _gps = new ArrayList(); + Iterator en = getFeatureGroups().iterator(); + int g = 0; + boolean valid = false; + while (en.hasNext()) + { + String gp = (String) en.next(); + if (checkGroupVisibility(gp, false)) + { + valid = true; + _gps.add(gp); + } + if (!valid) + { + return null; + } + else + { + gps = new String[_gps.size()]; + _gps.toArray(gps); + } + } + return gps; + } + +} diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java new file mode 100644 index 0000000..6e85b83 --- /dev/null +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java @@ -0,0 +1,77 @@ +package jalview.viewmodel.seqfeatures; + +import jalview.schemes.GraduatedColor; + +import java.util.Arrays; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.Map; +import java.util.concurrent.ConcurrentHashMap; + +public class FeatureRendererSettings implements Cloneable +{ + String[] renderOrder; + + Map featureGroups; + + Map featureColours; + + float transparency; + + Map featureOrder; + + public FeatureRendererSettings(String[] renderOrder, + Hashtable featureGroups, Hashtable featureColours, + float transparency, Hashtable featureOrder) + { + super(); + this.renderOrder = Arrays.copyOf(renderOrder,renderOrder.length); + this.featureGroups = new ConcurrentHashMap(featureGroups); + this.featureColours = new ConcurrentHashMap(featureColours); + this.transparency = transparency; + this.featureOrder = new ConcurrentHashMap(featureOrder); + } + + /** + * create an independent instance of the feature renderer settings + * + * @param fr + */ + public FeatureRendererSettings( + jalview.viewmodel.seqfeatures.FeatureRendererModel fr) + { + renderOrder = null; + featureGroups = new ConcurrentHashMap(); + featureColours = new ConcurrentHashMap(); + featureOrder = new ConcurrentHashMap(); + if (fr.renderOrder != null) + { + this.renderOrder = new String[fr.renderOrder.length]; + System.arraycopy(fr.renderOrder, 0, renderOrder, 0, + fr.renderOrder.length); + } + if (fr.featureGroups != null) + { + this.featureGroups = new ConcurrentHashMap(fr.featureGroups); + } + if (fr.featureColours != null) + { + this.featureColours = new ConcurrentHashMap(fr.featureColours); + } + Iterator en = fr.featureColours.keySet().iterator(); + while (en.hasNext()) + { + Object next = en.next(); + Object val = featureColours.get(next); + if (val instanceof GraduatedColor) + { + featureColours.put(next, new GraduatedColor((GraduatedColor) val)); + } + } + this.transparency = fr.transparency; + if (fr.featureOrder != null) + { + this.featureOrder = new ConcurrentHashMap(fr.featureOrder); + } + } +} \ No newline at end of file diff --git a/src/jalview/viewmodel/seqfeatures/FeatureSettingsModel.java b/src/jalview/viewmodel/seqfeatures/FeatureSettingsModel.java new file mode 100644 index 0000000..57d57da --- /dev/null +++ b/src/jalview/viewmodel/seqfeatures/FeatureSettingsModel.java @@ -0,0 +1,8 @@ +package jalview.viewmodel.seqfeatures; + +import jalview.api.FeatureSettingsModelI; + +public class FeatureSettingsModel implements FeatureSettingsModelI +{ + +} diff --git a/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java b/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java new file mode 100644 index 0000000..b04764c --- /dev/null +++ b/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java @@ -0,0 +1,94 @@ +package jalview.viewmodel.seqfeatures; + +import jalview.api.FeaturesDisplayedI; + +import java.util.Collection; +import java.util.HashSet; +import java.util.Iterator; + +public class FeaturesDisplayed implements FeaturesDisplayedI +{ + private HashSet featuresDisplayed = new HashSet(); + + private HashSet featuresRegistered = new HashSet(); + + public FeaturesDisplayed(FeaturesDisplayedI featuresDisplayed2) + { + Iterator fdisp = featuresDisplayed2.getVisibleFeatures(); + String ftype; + while (fdisp.hasNext()) + { + ftype = fdisp.next(); + featuresDisplayed.add(ftype); + featuresRegistered.add(ftype); + } + } + + public FeaturesDisplayed() + { + // TODO Auto-generated constructor stub + } + + @Override + public Iterator getVisibleFeatures() + { + return featuresDisplayed.iterator(); + } + + @Override + public boolean isVisible(String featureType) + { + return featuresDisplayed.contains(featureType); + } + + @Override + public boolean areVisible(Collection featureTypes) + { + return featuresDisplayed.containsAll(featureTypes); + } + + @Override + public void clear() + { + featuresDisplayed.clear(); + featuresRegistered.clear(); + } + + @Override + public void setAllVisible(Collection makeVisible) + { + featuresDisplayed.addAll(makeVisible); + featuresRegistered.addAll(makeVisible); + } + + @Override + public void setAllRegisteredVisible() + { + featuresDisplayed.addAll(featuresRegistered); + } + + @Override + public void setVisible(String featureType) + { + featuresDisplayed.add(featureType); + featuresRegistered.add(featureType); + } + + @Override + public boolean isRegistered(String type) + { + return featuresRegistered.contains(type); + } + + @Override + public int getVisibleFeatureCount() + { + return featuresDisplayed.size(); + } + + @Override + public int getRegisterdFeaturesCount() + { + return featuresRegistered.size(); + } +} diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java index edb56a9..d3682d4 100644 --- a/src/jalview/ws/AWSThread.java +++ b/src/jalview/ws/AWSThread.java @@ -28,7 +28,7 @@ import jalview.datamodel.AlignmentView; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.WebserviceInfo; -import jalview.gui.FeatureRenderer.FeatureRendererSettings; +import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import jalview.util.MessageManager; public abstract class AWSThread extends Thread diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java index 8a7bcbc..a778ab1 100644 --- a/src/jalview/ws/DasSequenceFeatureFetcher.java +++ b/src/jalview/ws/DasSequenceFeatureFetcher.java @@ -496,13 +496,13 @@ public class DasSequenceFeatureFetcher } catch (Exception ex) { Cache.log - .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org."); - Cache.log.info("Mapping feature from " + f.getBegin() + .warn("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org."); + Cache.log.warn("Mapping feature from " + f.getBegin() + " to " + f.getEnd() + " in dbref " + dbref.getAccessionId() + " in " + dbref.getSource()); - Cache.log.info("using das Source " + source); - Cache.log.info("Exception", ex); + Cache.log.warn("using das Source " + source); + Cache.log.warn("Exception", ex); } if (vf != null) @@ -626,7 +626,9 @@ public class DasSequenceFeatureFetcher Object[] nextSequence(jalviewSourceI dasSource, SequenceI seq) { if (cancelled) + { return null; + } DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs( seq.getDBRef(), new String[] { @@ -668,7 +670,9 @@ public class DasSequenceFeatureFetcher qstring.add(uprefs[j].getAccessionId()); } else + { System.out.println("IGNORE " + csys.getAuthority()); + } } } } @@ -839,7 +843,7 @@ public class DasSequenceFeatureFetcher { for (String note : feat.getNOTE()) { - desc += (String) note; + desc += note; } } diff --git a/src/jalview/ws/HttpClientUtils.java b/src/jalview/ws/HttpClientUtils.java index 229fa4e..1bdf64f 100644 --- a/src/jalview/ws/HttpClientUtils.java +++ b/src/jalview/ws/HttpClientUtils.java @@ -29,6 +29,7 @@ import java.util.List; import org.apache.http.HttpEntity; import org.apache.http.HttpResponse; +import org.apache.http.HttpVersion; import org.apache.http.NameValuePair; import org.apache.http.client.ClientProtocolException; import org.apache.http.client.HttpClient; @@ -40,6 +41,9 @@ import org.apache.http.entity.mime.content.FileBody; import org.apache.http.entity.mime.content.InputStreamBody; import org.apache.http.entity.mime.content.StringBody; import org.apache.http.impl.client.DefaultHttpClient; +import org.apache.http.params.BasicHttpParams; +import org.apache.http.params.CoreProtocolPNames; +import org.apache.http.params.HttpParams; /** * Helpful procedures for working with services via HTTPClient @@ -64,7 +68,10 @@ public class HttpClientUtils List vals) throws ClientProtocolException, IOException { - HttpClient httpclient = new DefaultHttpClient(); + HttpParams params = new BasicHttpParams(); + params.setParameter(CoreProtocolPNames.PROTOCOL_VERSION, + HttpVersion.HTTP_1_1); + HttpClient httpclient = new DefaultHttpClient(params); HttpPost httppost = new HttpPost(postUrl); UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8"); httppost.setEntity(ue); diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java index 1a96464..df0e091 100644 --- a/src/jalview/ws/jws1/JPredClient.java +++ b/src/jalview/ws/jws1/JPredClient.java @@ -20,18 +20,28 @@ */ package jalview.ws.jws1; +import jalview.analysis.AlignSeq; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.SeqCigar; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.WebserviceInfo; +import jalview.util.MessageManager; + import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.util.*; +import java.util.Hashtable; -import javax.swing.*; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; -import ext.vamsas.*; -import jalview.analysis.*; -import jalview.bin.*; -import jalview.datamodel.*; -import jalview.gui.*; -import jalview.util.MessageManager; +import ext.vamsas.Jpred; +import ext.vamsas.JpredServiceLocator; +import ext.vamsas.JpredSoapBindingStub; +import ext.vamsas.ServiceHandle; public class JPredClient extends WS1Client { @@ -291,7 +301,7 @@ public class JPredClient extends WS1Client WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred"; WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle, - WebServiceReference); + WebServiceReference, true); return wsInfo; } diff --git a/src/jalview/ws/jws1/WS1Client.java b/src/jalview/ws/jws1/WS1Client.java index 210e520..9001c61 100644 --- a/src/jalview/ws/jws1/WS1Client.java +++ b/src/jalview/ws/jws1/WS1Client.java @@ -92,7 +92,8 @@ public abstract class WS1Client extends WSClient implements WebserviceInfo wsInfo = null; if (!headless) { - wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference); + wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference, + true); } return wsInfo; } diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java index 6c438be..929581d 100644 --- a/src/jalview/ws/jws2/AADisorderClient.java +++ b/src/jalview/ws/jws2/AADisorderClient.java @@ -351,7 +351,7 @@ public class AADisorderClient extends JabawsCalcWorker implements { if (dispFeatures) { - jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap) + jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap) .cloneFeatureRenderer(); for (String ft : fc.keySet()) { diff --git a/src/jalview/ws/jws2/JabaWsServerQuery.java b/src/jalview/ws/jws2/JabaWsServerQuery.java index 74dce4d..b3aee55 100644 --- a/src/jalview/ws/jws2/JabaWsServerQuery.java +++ b/src/jalview/ws/jws2/JabaWsServerQuery.java @@ -180,7 +180,8 @@ public class JabaWsServerQuery implements Runnable jws2Discoverer.addInvalidServiceUrl(jwsserver); } ; - if (service != null) + if (service != null + && !Jws2InstanceFactory.ignoreService(srv.toString())) { noservices = false; Jws2Instance svc = null; @@ -212,7 +213,7 @@ public class JabaWsServerQuery implements Runnable else { jws2Discoverer.addInvalidServiceUrl(jwsserver); - Cache.log.info("Ignoring invalid Jws2 service url " + jwsserver); + Cache.log.warn("Ignoring invalid Jws2 service url " + jwsserver); } } catch (Exception e) { diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java index afefe65..751d330 100644 --- a/src/jalview/ws/jws2/Jws2Client.java +++ b/src/jalview/ws/jws2/Jws2Client.java @@ -20,17 +20,6 @@ */ package jalview.ws.jws2; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.util.List; - -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; - -import compbio.metadata.Argument; import jalview.api.AlignCalcWorkerI; import jalview.bin.Cache; import jalview.gui.AlignFrame; @@ -45,6 +34,18 @@ import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.WsParamSetI; import jalview.ws.uimodel.AlignAnalysisUIText; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.List; + +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.event.MenuEvent; +import javax.swing.event.MenuListener; + +import compbio.metadata.Argument; + /** * provides metadata for a jabaws2 service instance - resolves names, etc. * @@ -148,7 +149,7 @@ public abstract class Jws2Client extends jalview.ws.WSClient { return new WebserviceInfo(WebServiceJobTitle, WebServiceJobTitle + " using service hosted at " + serv.hosturl + "\n" - + (serv.description != null ? serv.description : "")); + + (serv.description != null ? serv.description : ""), false); } return null; } diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index a111d68..7a8eee9 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -705,7 +705,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } else { - Cache.log.info("Ignoring duplicate url " + url + " in " + Cache.log.warn("Ignoring duplicate url " + url + " in " + JWS2HOSTURLS + " list"); } } catch (MalformedURLException ex) diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java index 39be454..e7301a6 100644 --- a/src/jalview/ws/jws2/MsaWSClient.java +++ b/src/jalview/ws/jws2/MsaWSClient.java @@ -22,7 +22,6 @@ package jalview.ws.jws2; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentView; -import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.JvSwingUtils; @@ -175,47 +174,20 @@ public class MsaWSClient extends Jws2Client MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps, preserveOrder, seqdataset); - wsInfo.setthisService(msathread); - - msathread.start(); - - } - - private boolean isValidAlignment(AlignmentView av) - { - int validSeqCount = 0; - List seqs = av.getVisibleAlignment('c').getSequences(); // .getSequences(); - if (seqs.size() < 2) + if (msathread.hasValidInput()) { - JOptionPane - .showMessageDialog( - alignFrame, - "A minimum of two sequences is required to perform this operation", - "Invalid selection", JOptionPane.INFORMATION_MESSAGE); - - return false; + wsInfo.setthisService(msathread); + wsInfo.setVisible(true); + msathread.start(); } - - for (SequenceI seq : seqs) + else { - - if (seq.getSequenceAsString().matches("(-*[a-zA-Z]-*){3}[a-zA-Z-]*")) - { - ++validSeqCount; - } - if (validSeqCount > 1) - { - return true; - } + JOptionPane.showMessageDialog(alignFrame, + MessageManager.getString("info.invalid_msa_input_mininfo"), + MessageManager.getString("info.invalid_msa_notenough"), + JOptionPane.INFORMATION_MESSAGE); + wsInfo.setVisible(false); } - - JOptionPane - .showMessageDialog( - alignFrame, - "All selected sequence for this job must have a minimum of \nthree non-gap character to perform this operation", - "Invalid selection", JOptionPane.INFORMATION_MESSAGE); - - return false; } public static void main(String[] args) @@ -300,7 +272,7 @@ public class MsaWSClient extends Jws2Client { AlignmentView msa = alignFrame.gatherSequencesForAlignment(); - if (msa != null && isValidAlignment(msa)) + if (msa != null) { new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps, true, alignFrame.getViewport().getAlignment() @@ -324,10 +296,9 @@ public class MsaWSClient extends Jws2Client public void actionPerformed(ActionEvent e) { AlignmentView msa = alignFrame.gatherSequencesForAlignment(); - - if (msa != null && isValidAlignment(msa)) + if (msa != null) { - new MsaWSClient(service, null, null, true, alignFrame + new MsaWSClient(service, null, null, true, alignFrame .getTitle(), msa, withGaps, true, alignFrame .getViewport().getAlignment().getDataset(), alignFrame); } @@ -382,9 +353,10 @@ public class MsaWSClient extends Jws2Client AlignmentView msa = alignFrame .gatherSequencesForAlignment(); - if (msa != null && isValidAlignment(msa)) + if (msa != null) { - new MsaWSClient(service, preset, alignFrame.getTitle(), + MsaWSClient msac = new MsaWSClient(service, preset, + alignFrame.getTitle(), msa, false, true, alignFrame.getViewport() .getAlignment().getDataset(), alignFrame); } diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java index 5e8cb98..2bae428 100644 --- a/src/jalview/ws/jws2/MsaWSThread.java +++ b/src/jalview/ws/jws2/MsaWSThread.java @@ -20,7 +20,29 @@ */ package jalview.ws.jws2; -import java.util.*; +import jalview.analysis.AlignSeq; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.WebserviceInfo; +import jalview.util.MessageManager; +import jalview.ws.AWsJob; +import jalview.ws.JobStateSummary; +import jalview.ws.WSClientI; +import jalview.ws.jws2.dm.JabaWsParamSet; +import jalview.ws.params.WsParamSetI; + +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.Vector; import compbio.data.msa.MsaWS; import compbio.metadata.Argument; @@ -28,17 +50,6 @@ import compbio.metadata.ChunkHolder; import compbio.metadata.JobStatus; import compbio.metadata.Preset; -import jalview.analysis.*; -import jalview.bin.*; -import jalview.datamodel.*; -import jalview.gui.*; -import jalview.util.MessageManager; -import jalview.ws.AWsJob; -import jalview.ws.WSClientI; -import jalview.ws.JobStateSummary; -import jalview.ws.jws2.dm.JabaWsParamSet; -import jalview.ws.params.WsParamSetI; - class MsaWSThread extends AWS2Thread implements WSClientI { boolean submitGaps = false; // pass sequences including gaps to alignment @@ -221,7 +232,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI int ow = w, nw = w; for (i = 0, w = emptySeqs.size(); i < w; i++) { - String[] es = (String[]) emptySeqs.get(i); + String[] es = emptySeqs.get(i); if (es != null && es[1] != null) { int sw = es[1].length(); @@ -252,7 +263,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI } for (i = 0, w = emptySeqs.size(); i < w; i++) { - String[] es = (String[]) emptySeqs.get(i); + String[] es = emptySeqs.get(i); if (es[1] == null) { t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0], @@ -474,7 +485,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI SequenceI[][] conmsa = _msa.getVisibleContigs('-'); if (conmsa != null) { - int njobs = conmsa.length; + int nvalid = 0, njobs = conmsa.length; jobs = new MsaWSJob[njobs]; for (int j = 0; j < njobs; j++) { @@ -486,6 +497,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI { jobs[j] = new MsaWSJob(0, conmsa[j]); } + if (((MsaWSJob) jobs[j]).hasValidInput()) + { + nvalid++; + } ((MsaWSJob) jobs[j]).preset = preset; ((MsaWSJob) jobs[j]).arguments = paramset; ((MsaWSJob) jobs[j]).alignmentProgram = wsname; @@ -496,9 +511,20 @@ class MsaWSThread extends AWS2Thread implements WSClientI } wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader); } + validInput = nvalid > 0; } } + boolean validInput = false; + + /** + * + * @return true if the thread will perform a calculation + */ + public boolean hasValidInput() + { + return validInput; + } public boolean isCancellable() { return true; diff --git a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java index bcc7735..696dba3 100644 --- a/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java +++ b/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java @@ -20,18 +20,21 @@ */ package jalview.ws.jws2.jabaws2; -import java.util.HashMap; - -import compbio.data.msa.JABAService; import jalview.ws.jws2.AAConClient; import jalview.ws.jws2.JPred301Client; import jalview.ws.jws2.RNAalifoldClient; import jalview.ws.uimodel.AlignAnalysisUIText; +import java.util.HashMap; +import java.util.HashSet; + +import compbio.data.msa.JABAService; + public class Jws2InstanceFactory { private static HashMap aaConGUI; + private static HashSet ignoreGUI; private static String category_rewrite(String cat_name) { return (cat_name != null && cat_name.equals("Prediction")) ? "Secondary Structure Prediction" @@ -47,12 +50,27 @@ public class Jws2InstanceFactory AAConClient.getAlignAnalysisUITest()); aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(), RNAalifoldClient.getAlignAnalysisUITest()); + // disable the JPred301 client in jalview ... + ignoreGUI = new HashSet(); + ignoreGUI.add(compbio.ws.client.Services.JpredWS.toString()); aaConGUI.put(compbio.ws.client.Services.JpredWS.toString(), JPred301Client.getAlignAnalysisUITest()); } } /** + * exclusion list to avoid creating GUI elements for services we don't fully + * support + * + * @param serviceType + * @return + */ + public static boolean ignoreService(String serviceType) + { + init(); + return (ignoreGUI.contains(serviceType.toString())); + } + /** * construct a service instance and configure it with any additional * properties needed so Jalview can access it correctly * @@ -70,7 +88,6 @@ public class Jws2InstanceFactory init(); Jws2Instance svc = new Jws2Instance(jwsservers, serviceType, category_rewrite(name), description, service); - svc.aaui = aaConGUI.get(serviceType.toString()); return svc; } diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java index cd4bb23..5ce1d5d 100644 --- a/src/jalview/ws/rest/RestClient.java +++ b/src/jalview/ws/rest/RestClient.java @@ -20,17 +20,6 @@ */ package jalview.ws.rest; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.util.Hashtable; -import java.util.Vector; - -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; - import jalview.bin.Cache; import jalview.datamodel.AlignmentView; import jalview.gui.AlignFrame; @@ -44,6 +33,17 @@ import jalview.ws.WSClient; import jalview.ws.WSClientI; import jalview.ws.WSMenuEntryProviderI; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.Hashtable; +import java.util.Vector; + +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.event.MenuEvent; +import javax.swing.event.MenuListener; + /** * @author JimP * @@ -107,7 +107,7 @@ public class RestClient extends WSClient implements WSClientI, if (!headless) { wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n" - + WebServiceReference); + + WebServiceReference, true); wsInfo.setRenderAsHtml(true); } diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java new file mode 100644 index 0000000..1dbaa4a --- /dev/null +++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java @@ -0,0 +1,74 @@ +package jalview.analysis.scoremodels; + +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.io.FileLoader; +import jalview.io.FormatAdapter; + +import org.junit.Assert; +import org.junit.Test; + +public class FeatureScoreModelTest +{ + public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n"; + + int[] sf1 = new int[] + { 74, 74, 73, 73, 23, 23, -1, -1 }; + + int[] sf2 = new int[] + { -1, -1, 74, 75, -1, -1, 76, 77 }; + + int[] sf3 = new int[] + { -1, -1, -1, -1, -1, -1, 76, 77 }; + + @Test + public void testFeatureScoreModel() throws Exception + { + AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(alntestFile, + FormatAdapter.PASTE); + AlignmentI al = alf.getViewport().getAlignment(); + Assert.assertEquals(4, al.getHeight()); + Assert.assertEquals(5, al.getWidth()); + for (int i = 0; i < 4; i++) + { + SequenceI ds = al.getSequenceAt(i).getDatasetSequence(); + if (sf1[i * 2] > 0) + { + ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", "sf1", + sf1[i * 2], sf1[i * 2 + 1], "sf1")); + } + if (sf2[i * 2] > 0) + { + ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", "sf2", + sf2[i * 2], sf2[i * 2 + 1], "sf2")); + } + if (sf3[i * 2] > 0) + { + ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", "sf3", + sf3[i * 2], sf3[i * 2 + 1], "sf3")); + } + } + alf.setShowSeqFeatures(true); + alf.getFeatureRenderer().setVisible("sf1"); + alf.getFeatureRenderer().setVisible("sf2"); + alf.getFeatureRenderer().setVisible("sf3"); + alf.getFeatureRenderer().findAllFeatures(true); + Assert.assertEquals("Number of feature types", 3, alf + .getFeatureRenderer().getDisplayedFeatureTypes().length); + Assert.assertTrue(alf.getCurrentView().areFeaturesDisplayed()); + FeatureScoreModel fsm = new FeatureScoreModel(); + Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView() + .getAlignPanel())); + alf.selectAllSequenceMenuItem_actionPerformed(null); + float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView( + true)); + Assert.assertTrue("FER1_MESCR should be identical with RAPSA (2)", + dm[0][2] == 0f); + Assert.assertTrue( + "FER1_MESCR should be further from SPIOL (1) than it is from RAPSA (2)", + dm[0][1] > dm[0][2]); + + } +} diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java index d9101cf..3f91710 100644 --- a/test/jalview/datamodel/SequenceTest.java +++ b/test/jalview/datamodel/SequenceTest.java @@ -88,7 +88,8 @@ public class SequenceTest /** * Tests for addAlignmentAnnotation. Note this method has the side-effect of - * setting the sequenceRef on the annotation. + * setting the sequenceRef on the annotation. Adding the same annotation twice + * should be ignored. */ @Test public void testAddAlignmentAnnotation() @@ -102,5 +103,21 @@ public class SequenceTest AlignmentAnnotation[] anns = seq.getAnnotation(); assertEquals(1, anns.length); assertSame(annotation, anns[0]); + + // re-adding does nothing + seq.addAlignmentAnnotation(annotation); + anns = seq.getAnnotation(); + assertEquals(1, anns.length); + assertSame(annotation, anns[0]); + + // an identical but different annotation can be added + final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a", + "b", 2d); + seq.addAlignmentAnnotation(annotation2); + anns = seq.getAnnotation(); + assertEquals(2, anns.length); + assertSame(annotation, anns[0]); + assertSame(annotation2, anns[1]); + } } diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java new file mode 100644 index 0000000..7dfbba1 --- /dev/null +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -0,0 +1,92 @@ +package jalview.ext.rbvi.chimera; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + +import java.awt.Color; +import java.util.Arrays; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; + +import org.junit.Test; + +public class ChimeraCommandsTest +{ + @Test + public void testAddColourRange() + { + Map>>> map = new LinkedHashMap>>>(); + ChimeraCommands.addColourRange(map, Color.pink, 1, 2, 4, "A"); + ChimeraCommands.addColourRange(map, Color.pink, 1, 8, 8, "A"); + ChimeraCommands.addColourRange(map, Color.pink, 1, 5, 7, "B"); + ChimeraCommands.addColourRange(map, Color.red, 1, 3, 5, "A"); + ChimeraCommands.addColourRange(map, Color.red, 0, 1, 4, "B"); + ChimeraCommands.addColourRange(map, Color.orange, 0, 5, 9, "C"); + + // three colours mapped + assertEquals(3, map.keySet().size()); + + // Red has two models, Pink and Orange one each + assertEquals(2, map.get(Color.red).keySet().size()); + assertEquals(1, map.get(Color.orange).keySet().size()); + assertEquals(1, map.get(Color.pink).keySet().size()); + + // pink model 1 has two chains, red.0 / red.1 / orange.0 one each + assertEquals(2, map.get(Color.pink).get(1).keySet().size()); + assertEquals(1, map.get(Color.red).get(0).keySet().size()); + assertEquals(1, map.get(Color.red).get(1).keySet().size()); + assertEquals(1, map.get(Color.orange).get(0).keySet().size()); + + // inspect positions + List posList = map.get(Color.pink).get(1).get("A"); + assertEquals(2, posList.size()); + assertTrue(Arrays.equals(new int[] + { 2, 4 }, posList.get(0))); + assertTrue(Arrays.equals(new int[] + { 8, 8 }, posList.get(1))); + + posList = map.get(Color.pink).get(1).get("B"); + assertEquals(1, posList.size()); + assertTrue(Arrays.equals(new int[] + { 5, 7 }, posList.get(0))); + + posList = map.get(Color.red).get(0).get("B"); + assertEquals(1, posList.size()); + assertTrue(Arrays.equals(new int[] + { 1, 4 }, posList.get(0))); + + posList = map.get(Color.red).get(1).get("A"); + assertEquals(1, posList.size()); + assertTrue(Arrays.equals(new int[] + { 3, 5 }, posList.get(0))); + + posList = map.get(Color.orange).get(0).get("C"); + assertEquals(1, posList.size()); + assertTrue(Arrays.equals(new int[] + { 5, 9 }, posList.get(0))); + } + + @Test + public void testBuildColourCommands() + { + + Map>>> map = new LinkedHashMap>>>(); + ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A"); + ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B"); + ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A"); + ChimeraCommands.addColourRange(map, Color.blue, 1, 1, 1, "A"); + ChimeraCommands.addColourRange(map, Color.blue, 1, 4, 7, "B"); + ChimeraCommands.addColourRange(map, Color.yellow, 1, 8, 8, "A"); + ChimeraCommands.addColourRange(map, Color.yellow, 1, 3, 5, "A"); + ChimeraCommands.addColourRange(map, Color.red, 0, 3, 5, "A"); + + // Colours should appear in the Chimera command in the order in which + // they were added; within colour, by model, by chain, and positions as + // added + String command = ChimeraCommands.buildColourCommands(map).get(0); + assertEquals( + "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:8.A,3-5.A; color #ff0000 #0:3-5.A", + command); + } +} diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java index 1d219df..f7b1482 100644 --- a/test/jalview/gui/PopupMenuTest.java +++ b/test/jalview/gui/PopupMenuTest.java @@ -7,6 +7,7 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; +import jalview.io.FormatAdapter; import jalview.util.MessageManager; import java.awt.Component; @@ -42,7 +43,7 @@ public class PopupMenuTest @Before public void setUp() throws IOException { - alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA, + alignment = new FormatAdapter().readFile(TEST_DATA, AppletFormatAdapter.PASTE, "FASTA"); AlignFrame af = new AlignFrame(alignment, 700, 500); parentPanel = new AlignmentPanel(af, af.getViewport()); @@ -83,14 +84,13 @@ public class PopupMenuTest public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations() { JMenuItem menu = new JMenuItem(); - List seqs = new ArrayList(); /* * Initial state is that sequences have annotations, and have dataset * sequences, but the dataset sequences have no annotations. Hence nothing * to add. */ - seqs = parentPanel.getAlignment().getSequences(); + List seqs = parentPanel.getAlignment().getSequences(); testee.configureReferenceAnnotationsMenu(menu, seqs); assertFalse(menu.isEnabled()); @@ -105,12 +105,12 @@ public class PopupMenuTest public void testConfigureReferenceAnnotationsMenu_alreadyAdded() { JMenuItem menu = new JMenuItem(); - List seqs = new ArrayList(); + List seqs = parentPanel.getAlignment().getSequences(); + + // make up new annotations and add to dataset sequences, sequences and + // alignment + attachReferenceAnnotations(seqs, true, true); - seqs = parentPanel.getAlignment().getSequences(); - // copy annotation from sequence to dataset - seqs.get(1).getDatasetSequence() - .addAlignmentAnnotation(seqs.get(1).getAnnotation()[0]); testee.configureReferenceAnnotationsMenu(menu, seqs); assertFalse(menu.isEnabled()); } @@ -126,28 +126,104 @@ public class PopupMenuTest { JMenuItem menu = new JMenuItem(); List seqs = parentPanel.getAlignment().getSequences(); + // make up new annotations and add to dataset sequences + attachReferenceAnnotations(seqs, false, false); + + testee.configureReferenceAnnotationsMenu(menu, seqs); + assertTrue(menu.isEnabled()); + String expected = "

Action	Set the colourscheme for the alignment. This can be any of the built-in colourschemes, a name of a predefined colourscheme - (defined in the jalview properties file), or an 'inline' colourscheme + (defined in the Jalview properties file), or an 'inline' colourscheme (see the applet's colour parameter for more information).
+ -jabaws URL +	+ Specify the URL of the preferred JABAWS server +
-vdoc VAMSAS DOCUMENT FILE/URL @@ -196,7 +203,7 @@
-svg FILE	Create Support Vector Graphics file FILE from alignment.	Create Scalable Vector Graphics file FILE from alignment.