From: gmungoc Date: Fri, 25 Nov 2016 14:21:34 +0000 (+0000) Subject: Merge branch 'develop' into trialMerge X-Git-Tag: Release_2_10_3b1~403 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git Merge branch 'develop' into trialMerge Conflicts: src/jalview/appletgui/AlignFrame.java src/jalview/appletgui/AppletJmol.java src/jalview/appletgui/AppletJmolBinding.java src/jalview/appletgui/ExtJmol.java src/jalview/datamodel/PDBEntry.java src/jalview/ext/ensembl/EnsemblRestClient.java src/jalview/ext/jmol/JalviewJmolBinding.java src/jalview/ext/jmol/JmolParser.java src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java src/jalview/gui/AlignFrame.java src/jalview/gui/AppJmolBinding.java src/jalview/gui/Desktop.java src/jalview/gui/FeatureSettings.java src/jalview/gui/Jalview2XML.java src/jalview/gui/JalviewChimeraBindingModel.java src/jalview/gui/StructureChooser.java src/jalview/io/AppletFormatAdapter.java src/jalview/io/BioJsHTMLOutput.java src/jalview/io/HTMLOutput.java src/jalview/io/HtmlSvgOutput.java src/jalview/io/StructureFile.java src/jalview/structure/StructureSelectionManager.java src/jalview/structures/models/AAStructureBindingModel.java src/jalview/ws/dbsources/Pdb.java src/jalview/ws/dbsources/Xfam.java test/MCview/PDBfileTest.java test/jalview/datamodel/AlignmentTest.java test/jalview/ext/jmol/JmolParserTest.java test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java test/jalview/gui/AlignViewportTest.java test/jalview/io/FeaturesFileTest.java test/jalview/io/Jalview2xmlTests.java test/jalview/io/PfamFormatInputTest.java test/jalview/io/gff/ExonerateHelperTest.java test/jalview/structure/Mapping.java test/jalview/structures/models/AAStructureBindingModelTest.java --- 7d67fb613ec026dc9a265e351e7fab542e3f1d61 diff --cc src/jalview/api/AlignViewControllerI.java index b868ee5,8ed2c95..a7ec69e --- a/src/jalview/api/AlignViewControllerI.java +++ b/src/jalview/api/AlignViewControllerI.java @@@ -96,7 -94,19 +96,19 @@@ public interface AlignViewController * @return true if parsing resulted in something being imported to the view or * dataset */ - public boolean parseFeaturesFile(String file, String protocol, + public boolean parseFeaturesFile(String file, DataSourceType sourceType, boolean relaxedIdMatching); + /** + * mark columns containing highlighted regions (e.g. from search, structure + * highlight, or a mouse over event in another viewer) + * + * @param invert + * @param extendCurrent + * @param toggle + * @return + */ + boolean markHighlightedColumns(boolean invert, boolean extendCurrent, + boolean toggle); + } diff --cc src/jalview/appletgui/AlignFrame.java index fcdf9d2,122afa8..f830fe6 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@@ -358,14 -355,14 +357,14 @@@ public class AlignFrame extends Embmenu * * @param file * file URL, content, or other resolvable path - * @param paste - * @param type ++ * @param sourceType * is protocol for accessing data referred to by file * @param autoenabledisplay * when true, display features flag will be automatically enabled if * features are loaded * @return true if data parsed as a features file */ - public boolean parseFeaturesFile(String file, DataSourceType paste, - public boolean parseFeaturesFile(String file, String type, ++ public boolean parseFeaturesFile(String file, DataSourceType sourceType, boolean autoenabledisplay) { boolean featuresFile = false; @@@ -375,7 -372,7 +374,7 @@@ .getFeatureRenderer().getFeatureColours(); boolean relaxedIdMatching = viewport.applet.getDefaultParameter( "relaxedidmatch", false); - featuresFile = new FeaturesFile(file, paste).parse( - featuresFile = new FeaturesFile(file, type).parse( ++ featuresFile = new FeaturesFile(file, sourceType).parse( viewport.getAlignment(), colours, true, relaxedIdMatching); } catch (Exception ex) { @@@ -4082,16 -4071,10 +4072,16 @@@ System.err .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); } - if (protocol == null || protocol.trim().length() == 0 - || protocol.equals("null")) + if (protocol == null) { - String sourceType = pdb.getProperty().get("protocol"); - protocol = (String) pdb.getProperty("protocol"); ++ String sourceType = (String) pdb.getProperty("protocol"); + try + { + protocol = DataSourceType.valueOf(sourceType); + } catch (IllegalArgumentException e) + { + // ignore + } if (protocol == null) { System.err.println("Couldn't work out protocol to open structure: " diff --cc src/jalview/appletgui/AppletJmol.java index 18e7d1a,133cc94..9d4779c --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@@ -291,15 -289,12 +290,12 @@@ public class AppletJmol extends Embmenu closeViewer(); } }); - if (pdbentry.getProperty() == null) - { - pdbentry.setProperty(new Hashtable()); - pdbentry.getProperty().put("protocol", protocol.toString()); - } + pdbentry.setProperty("protocol", protocol); - if (pdbentry.getFile() != null) ++ { // import structure data from pdbentry.getFile based on given protocol - if (protocol.equals(AppletFormatAdapter.PASTE)) + if (protocol == DataSourceType.PASTE) { // TODO: JAL-623 : correctly record file contents for matching up later // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode()); diff --cc src/jalview/appletgui/AppletJmolBinding.java index 92dff7b,684d357..f938cad --- a/src/jalview/appletgui/AppletJmolBinding.java +++ b/src/jalview/appletgui/AppletJmolBinding.java @@@ -46,9 -43,9 +44,9 @@@ class AppletJmolBinding extends Jalview public AppletJmolBinding(AppletJmol appletJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry, - SequenceI[][] seq, String[][] chains, DataSourceType protocol) - SequenceI[][] seq, String protocol) ++ SequenceI[][] seq, DataSourceType protocol) { - super(sSm, pdbentry, seq, chains, protocol); + super(sSm, pdbentry, seq, protocol); appletJmolBinding = appletJmol; } diff --cc src/jalview/appletgui/ExtJmol.java index a402ae0,5ffbaa4..189fe88 --- a/src/jalview/appletgui/ExtJmol.java +++ b/src/jalview/appletgui/ExtJmol.java @@@ -49,12 -48,12 +49,12 @@@ public class ExtJmol extends JalviewJmo private AlignmentPanel ap; - protected ExtJmol(jalview.appletgui.AlignFrame alframe, + protected ExtJmol(AlignFrame alframe, - PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains, + PDBEntry[] pdbentry, SequenceI[][] seq, - String protocol) + DataSourceType protocol) { super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq, - chains, protocol); + protocol); } public ExtJmol(Viewer viewer, AlignmentPanel alignPanel, diff --cc src/jalview/bin/Jalview.java index 1ab837f,bcb4e7b..39c0a5b --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@@ -654,7 -657,28 +668,28 @@@ public class Jalvie System.out.println("Creating HTML image: " + file); continue; } - else if (format.equalsIgnoreCase("biojsmsa")) ++ else if (outputFormat.equalsIgnoreCase("biojsmsa")) + { + if (file == null) + { + System.err.println("The output html file must not be null"); + return; + } + try + { + BioJsHTMLOutput + .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); + } catch (URISyntaxException e) + { + e.printStackTrace(); + } + BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); + bjs.exportHTML(file); + System.out.println("Creating BioJS MSA Viwer HTML file: " + + file); + continue; + } - else if (format.equalsIgnoreCase("imgMap")) + else if (outputFormat.equalsIgnoreCase("imgMap")) { af.createImageMap(new File(file), imageName); System.out.println("Creating image map: " + file); diff --cc src/jalview/datamodel/PDBEntry.java index 37dfdbf,9c3a8e7..97fb08d --- a/src/jalview/datamodel/PDBEntry.java +++ b/src/jalview/datamodel/PDBEntry.java @@@ -30,39 -44,43 +44,63 @@@ public class PDBEntr private String id; - private String chainCode; - public enum Type { - PDB, MMCIF, FILE; + // TODO is FILE needed; if not is this needed or can we + // use FileFormatI for PDB, MMCIF? + PDB("pdb", "xml"), MMCIF("mmcif", "mmcif"), FILE("?", "?"); + String ext; + + String format; + + private Type(String fmt, String ex) + { + format = fmt; + ext = ex; + } + + public String getFormat() + { + return format; + } + public String getExtension() + { + return ext; + } - } + - Hashtable properties; + /** + * case insensitive matching for Type enum + * + * @param value + * @return + */ + public static Type getType(String value) + { + for (Type t : Type.values()) + { + if (t.toString().equalsIgnoreCase(value)) + { + return t; + } + } + return null; + } - /* - * (non-Javadoc) - * - * @see java.lang.Object#equals(java.lang.Object) + /** + * case insensitive equivalence for strings resolving to PDBEntry type + * + * @param t + * @return + */ + public boolean matches(String t) + { + return (this.toString().equalsIgnoreCase(t)); + } + } + - + /** + * Answers true if obj is a PDBEntry with the same id and chain code (both + * ignoring case), file, type and properties */ @Override public boolean equals(Object obj) diff --cc src/jalview/ext/ensembl/EnsemblRestClient.java index 653d5d5,5903f69..8ee6aaf --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@@ -1,6 -1,25 +1,26 @@@ + /* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ext.ensembl; +import jalview.io.DataSourceType; import jalview.io.FileParse; import jalview.util.StringUtils; @@@ -207,9 -238,14 +239,14 @@@ abstract class EnsemblRestClient extend throws IOException { URL url = getUrl(ids); - + BufferedReader reader = getHttpResponse(url, ids); + if (reader == null) + { + // request failed + return null; + } - FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST"); + FileParse fp = new FileParse(reader, url.toString(), DataSourceType.URL); return fp; } diff --cc src/jalview/ext/jmol/JalviewJmolBinding.java index 3ee8a34,7a394f7..2d2d10e --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@@ -103,10 -97,10 +97,10 @@@ public abstract class JalviewJmolBindin public Viewer viewer; public JalviewJmolBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, - String protocol) + DataSourceType protocol) { - super(ssm, pdbentry, sequenceIs, chains, protocol); + super(ssm, pdbentry, sequenceIs, protocol); /* * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(), * "jalviewJmol", ap.av.applet .getDocumentBase(), diff --cc src/jalview/ext/jmol/JmolParser.java index 858aac7,180da8f..f08e40e --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@@ -22,8 -22,8 +22,9 @@@ package jalview.ext.jmol import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; + import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; import jalview.io.FileParse; import jalview.io.StructureFile; import jalview.schemes.ResidueProperties; @@@ -60,15 -59,12 +60,13 @@@ public class JmolParser extends Structu { Viewer viewer = null; - public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr, - boolean externalSecStr, String inFile, DataSourceType sourceType) - public JmolParser(String inFile, String type) throws IOException ++ public JmolParser(String inFile, DataSourceType sourceType) + throws IOException { - super(inFile, type); + super(inFile, sourceType); } - public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr, - boolean externalSecStr, FileParse fp) throws IOException + public JmolParser(FileParse fp) throws IOException { super(fp); } diff --cc src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index dca7038,4a9bf5f..b009948 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@@ -64,6 -64,9 +65,10 @@@ public abstract class JalviewChimeraBin private static final String ALPHACARBON = "CA"; + private List chainNames = new ArrayList(); + + private Hashtable chainFile = new Hashtable(); ++ /* * Object through which we talk to Chimera */ @@@ -193,14 -191,13 +193,12 @@@ * @param ssm * @param pdbentry * @param sequenceIs * @param protocol */ public JalviewChimeraBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, - DataSourceType protocol) - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol) ++ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol) { - super(ssm, pdbentry, sequenceIs, chains, protocol); + super(ssm, pdbentry, sequenceIs, protocol); viewer = new ChimeraManager( new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); } diff --cc src/jalview/gui/AlignFrame.java index 8cc1dd5,6a637e3..f31a220 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@@ -5031,9 -4826,11 +4830,12 @@@ public class AlignFrame extends GAlignF @Override public void drop(DropTargetDropEvent evt) { + // JAL-1552 - acceptDrop required before getTransferable call for + // Java's Transferable for native dnd + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - java.util.List files = new ArrayList(), protocols = new ArrayList(); + List files = new ArrayList(); + List protocols = new ArrayList(); try { @@@ -5099,7 -4896,7 +4901,7 @@@ } if (type != null) { - if (FileFormat.PDB.equals(type)) - if (StructureFile.isStructureFile(type)) ++ if (FileFormat.PDB.equals(type) || FileFormat.MMCif.equals(type)) { filesmatched.add(new Object[] { file, protocol, mtch }); continue; diff --cc src/jalview/gui/AppJmolBinding.java index 6e520e5,546890e..4d7f7cf --- a/src/jalview/gui/AppJmolBinding.java +++ b/src/jalview/gui/AppJmolBinding.java @@@ -42,10 -41,9 +42,9 @@@ public class AppJmolBinding extends Jal private FeatureRenderer fr = null; public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, - DataSourceType protocol) - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol) ++ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol) { - super(sSm, pdbentry, sequenceIs, chains, protocol); + super(sSm, pdbentry, sequenceIs, protocol); appJmolWindow = appJmol; } diff --cc src/jalview/gui/ChimeraViewFrame.java index a114f31,fe12f40..ab23e62 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@@ -28,9 -28,10 +28,10 @@@ import jalview.datamodel.PDBEntry import jalview.datamodel.SequenceI; import jalview.ext.rbvi.chimera.JalviewChimeraBinding; import jalview.gui.StructureViewer.ViewerType; -import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; + import jalview.io.StructureFile; import jalview.schemes.BuriedColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.HelixColourScheme; diff --cc src/jalview/gui/Desktop.java index 3fa5387,28606f1..2e8644e --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@@ -955,9 -950,12 +953,12 @@@ public class Desktop extends jalview.jb public void drop(DropTargetDropEvent evt) { boolean success = true; + // JAL-1552 - acceptDrop required before getTransferable call for + // Java's Transferable for native dnd + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - java.util.List files = new ArrayList(); - java.util.List protocols = new ArrayList(); + List files = new ArrayList(); + List protocols = new ArrayList(); try { @@@ -2189,8 -2172,9 +2191,8 @@@ if (v_client != null) { JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), "vdj", - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ - new String[] { "Vamsas Document" }, "Vamsas Document"); ++ Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ + "Vamsas Document", "Vamsas Document"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@@ -2246,7 -2230,7 +2248,7 @@@ */ public void setVamsasUpdate(boolean b) { -- jalview.bin.Cache.log.debug("Setting gui for Vamsas update " ++ Cache.log.debug("Setting gui for Vamsas update " + (b ? "in progress" : "finished")); if (vamUpdate != null) @@@ -3213,9 -3273,8 +3292,8 @@@ for (Object file : (List) t .getTransferData(DataFlavor.javaFileListFlavor)) { - files.add(((File)file).toString()); + files.add(((File) file).toString()); - protocols.add(FormatAdapter.FILE); + protocols.add(DataSourceType.FILE); } } else diff --cc src/jalview/gui/Jalview2XML_V1.java index 4a582de,3b39be7..5cd3bb2 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@@ -35,10 -36,8 +36,9 @@@ import jalview.binding.Tree import jalview.binding.UserColours; import jalview.binding.Viewport; import jalview.datamodel.PDBEntry; +import jalview.io.FileFormat; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; - import jalview.schemes.ResidueProperties; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; import jalview.util.jarInputStreamProvider; diff --cc src/jalview/gui/JalviewChimeraBindingModel.java index 76d2703,78ab68d..a399db3 --- a/src/jalview/gui/JalviewChimeraBindingModel.java +++ b/src/jalview/gui/JalviewChimeraBindingModel.java @@@ -33,12 -32,12 +33,12 @@@ public class JalviewChimeraBindingMode private FeatureRenderer fr = null; + public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame, StructureSelectionManager ssm, PDBEntry[] pdbentry, - SequenceI[][] sequenceIs, String[][] chains, - DataSourceType protocol) - SequenceI[][] sequenceIs, String protocol) ++ SequenceI[][] sequenceIs, DataSourceType protocol) { - super(ssm, pdbentry, sequenceIs, chains, protocol); + super(ssm, pdbentry, sequenceIs, protocol); cvf = chimeraViewFrame; } diff --cc src/jalview/gui/StructureChooser.java index 3581cf9,21b6e4f..c6ba8e9 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@@ -32,8 -32,8 +32,9 @@@ import jalview.fts.api.FTSRestClientI import jalview.fts.core.FTSRestRequest; import jalview.fts.core.FTSRestResponse; import jalview.fts.service.pdb.PDBFTSRestClient; +import jalview.io.DataSourceType; import jalview.jbgui.GStructureChooser; + import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; import jalview.ws.DBRefFetcher; @@@ -65,8 -65,6 +66,8 @@@ import javax.swing.table.AbstractTableM public class StructureChooser extends GStructureChooser implements IProgressIndicator { - private boolean structuresDiscovered = false; ++ private static int MAX_QLENGTH = 7820; + private SequenceI selectedSequence; private SequenceI[] selectedSequences; @@@ -83,6 -81,10 +84,8 @@@ private boolean isValidPBDEntry; + private boolean cachedPDBExists; + - private static int MAX_QLENGHT = 7820; - public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@@ -253,7 -261,8 +262,8 @@@ StringBuilder queryBuilder = new StringBuilder(); Set seqRefs = new LinkedHashSet(); - if (seq.getAllPDBEntries() != null) + if (seq.getAllPDBEntries() != null - && queryBuilder.length() < MAX_QLENGHT) ++ && queryBuilder.length() < MAX_QLENGTH) { for (PDBEntry entry : seq.getAllPDBEntries()) { @@@ -272,7 -279,8 +280,8 @@@ { for (DBRefEntry dbRef : seq.getDBRefs()) { - if (isValidSeqName(getDBRefId(dbRef))) + if (isValidSeqName(getDBRefId(dbRef)) - && queryBuilder.length() < MAX_QLENGHT) ++ && queryBuilder.length() < MAX_QLENGTH) { if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) { @@@ -732,76 -751,74 +752,74 @@@ int pdbIdColIndex = getResultTable().getColumn("PDB Id") .getModelIndex(); int refSeqColIndex = getResultTable().getColumn("Ref Sequence") - .getModelIndex(); + .getModelIndex(); int[] selectedRows = getResultTable().getSelectedRows(); - PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; - ArrayList selectedSeqsToView = new ArrayList(); - for (int row : selectedRows) - { + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + int count = 0; - ArrayList selectedSeqsToView = new ArrayList(); ++ List selectedSeqsToView = new ArrayList(); + for (int row : selectedRows) + { String pdbIdStr = getResultTable().getValueAt(row, - pdbIdColIndex) - .toString(); + pdbIdColIndex).toString(); SequenceI selectedSeq = (SequenceI) getResultTable() - .getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); + .getValueAt(row, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr); if (pdbEntry == null) { pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries()); } - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); - pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.PDB); - selectedSeq.getDatasetSequence().addPDBId(pdbEntry); - } - pdbEntriesToView[count++] = pdbEntry; - } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); + pdbEntry.setId(pdbIdStr); + pdbEntry.setType(PDBEntry.Type.PDB); + selectedSeq.getDatasetSequence().addPDBId(pdbEntry); + } + pdbEntriesToView[count++] = pdbEntry; + } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); - } - else if (currentView == VIEWS_LOCAL_PDB) - { - int[] selectedRows = tbl_local_pdb.getSelectedRows(); - PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; - int count = 0; + } + else if (currentView == VIEWS_LOCAL_PDB) + { + int[] selectedRows = tbl_local_pdb.getSelectedRows(); + PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; + int count = 0; int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id") .getModelIndex(); - int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") - .getModelIndex(); - ArrayList selectedSeqsToView = new ArrayList(); - for (int row : selectedRows) - { - PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, - pdbIdColIndex); - pdbEntriesToView[count++] = pdbEntry; - SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row, - refSeqColIndex); - selectedSeqsToView.add(selectedSeq); - } - SequenceI[] selectedSeqs = selectedSeqsToView - .toArray(new SequenceI[selectedSeqsToView.size()]); + int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") + .getModelIndex(); - ArrayList selectedSeqsToView = new ArrayList(); ++ List selectedSeqsToView = new ArrayList(); + for (int row : selectedRows) + { + PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, + pdbIdColIndex); + pdbEntriesToView[count++] = pdbEntry; + SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt( + row, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); + } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs); - } - else if (currentView == VIEWS_ENTER_ID) - { - SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) - { - selectedSequence = userSelectedSeq; - } + } + else if (currentView == VIEWS_ENTER_ID) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } - String pdbIdStr = txt_search.getText(); - PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); - if (pdbEntry == null) - { - pdbEntry = new PDBEntry(); + String pdbIdStr = txt_search.getText(); + PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); + if (pdbEntry == null) + { + pdbEntry = new PDBEntry(); if (pdbIdStr.split(":").length > 1) { pdbEntry.setId(pdbIdStr.split(":")[0]); @@@ -811,26 -828,26 +829,26 @@@ { pdbEntry.setId(pdbIdStr); } - pdbEntry.setType(PDBEntry.Type.PDB); - selectedSequence.getDatasetSequence().addPDBId(pdbEntry); - } + pdbEntry.setType(PDBEntry.Type.PDB); + selectedSequence.getDatasetSequence().addPDBId(pdbEntry); + } - PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; + PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; launchStructureViewer(ssm, pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); - } - else if (currentView == VIEWS_FROM_FILE) - { - SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) - { - selectedSequence = userSelectedSeq; - } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - jalview.io.AppletFormatAdapter.FILE, - selectedSequence, true, Desktop.instance); + } + else if (currentView == VIEWS_FROM_FILE) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + PDBEntry fileEntry = new AssociatePdbFileWithSeq() + .associatePdbWithSeq(selectedPdbFileName, + DataSourceType.FILE, + selectedSequence, true, Desktop.instance); launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new SequenceI[] { selectedSequence }); diff --cc src/jalview/io/AppletFormatAdapter.java index 4ffb86d,9695891..74fd422 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@@ -205,9 -290,7 +205,7 @@@ public class AppletFormatAdapte { StructureImportSettings.addSettings(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct); - alignFile = new JmolParser(annotFromStructure, - localSecondaryStruct, serviceSecondaryStruct, inFile, - sourceType); - alignFile = new jalview.ext.jmol.JmolParser(inFile, type); ++ alignFile = new JmolParser(inFile, sourceType); } else { diff --cc src/jalview/io/FileFormat.java index d0ce86e,0000000..d52045c mode 100644,000000..100644 --- a/src/jalview/io/FileFormat.java +++ b/src/jalview/io/FileFormat.java @@@ -1,611 -1,0 +1,594 @@@ +package jalview.io; + +import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.ext.jmol.JmolParser; +import jalview.structure.StructureImportSettings; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +public enum FileFormat implements FileFormatI +{ + Fasta("Fasta", "fa, fasta, mfa, fastq", true, true) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new FastaFile(inFile, sourceType); + } + + @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new FastaFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new FastaFile(); + } + }, + Pfam("PFAM", "pfam", true, true) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new PfamFile(inFile, sourceType); + } + + @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new PfamFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new PfamFile(); + } + }, + Stockholm("Stockholm", "sto,stk", true, true) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new StockholmFile(inFile, sourceType); + } + @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new StockholmFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new StockholmFile(al); + } + + }, + + PIR("PIR", "pir", true, true) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new PIRFile(inFile, sourceType); + } + @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new PIRFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new PIRFile(); + } + }, + BLC("BLC", "BLC", true, true) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new BLCFile(inFile, sourceType); + } @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new BLCFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new BLCFile(); + } + }, + AMSA("AMSA", "amsa", true, true) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new AMSAFile(inFile, sourceType); + } + + @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new AMSAFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new AMSAFile(al); + } + }, + Html("HTML", "html", true, false) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new HtmlFile(inFile, sourceType); + } @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new HtmlFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new HtmlFile(); + } + + @Override + public boolean isComplexAlignFile() + { + return true; + } + + }, + Rnaml("RNAML", "xml,rnaml", true, false) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new RnamlFile(inFile, sourceType); + } @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new RnamlFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new RnamlFile(); + } + + }, + Json("JSON","json", true, true) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new JSONFile(inFile, sourceType); + } @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new JSONFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new JSONFile(); + } + + @Override + public boolean isComplexAlignFile() + { + return true; + } + + }, + Pileup("PileUp", "pileup", true, true) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new PileUpfile(inFile, sourceType); + } @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new PileUpfile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new PileUpfile(); + } + + }, + MSF("MSF", "msf", true, true) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new MSFfile(inFile, sourceType); + } @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new MSFfile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new MSFfile(); + } + + }, + Clustal("Clustal", "aln", true, true) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new ClustalFile(inFile, sourceType); + } @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new ClustalFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new ClustalFile(); + } + }, + Phylip("PHYLIP", "phy", true, true) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new PhylipFile(inFile, sourceType); + } + + @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new PhylipFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new PhylipFile(); + } + }, + Jnet("JnetFile", "", false, false) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + JPredFile af = new JPredFile(inFile, sourceType); + af.removeNonSequences(); + return af; + } + + @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + JPredFile af = new JPredFile(source); + af.removeNonSequences(); + return af; + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return null; // todo is this called? + } + + }, + Features("GFF or Jalview features", "gff2,gff3", true, false) + { + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return new FeaturesFile(true, inFile, sourceType); + } + + @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return new FeaturesFile(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new FeaturesFile(); + } + }, + PDB("PDB", "pdb,ent", true, false) + { + + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + // TODO obtain config value from preference settings. + // Set value to 'true' to test PDB processing with Jmol: JAL-1213 + boolean isParseWithJMOL = StructureImportSettings + .getDefaultStructureFileFormat() != PDBEntry.Type.PDB; + if (isParseWithJMOL) + { - return new JmolParser( - StructureImportSettings.isVisibleChainAnnotation(), - StructureImportSettings.isProcessSecondaryStructure(), - StructureImportSettings.isExternalSecondaryStructure(), - inFile, - sourceType); ++ return new JmolParser(inFile, sourceType); + } + else + { + StructureImportSettings.setShowSeqFeatures(true); + return new MCview.PDBfile( + StructureImportSettings.isVisibleChainAnnotation(), + StructureImportSettings.isProcessSecondaryStructure(), + StructureImportSettings.isExternalSecondaryStructure(), + inFile, + sourceType); + } + } + + @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + boolean isParseWithJMOL = StructureImportSettings + .getDefaultStructureFileFormat() != PDBEntry.Type.PDB; + if (isParseWithJMOL) + { - return new JmolParser( - StructureImportSettings.isVisibleChainAnnotation(), - StructureImportSettings.isProcessSecondaryStructure(), - StructureImportSettings.isExternalSecondaryStructure(), - source); ++ return new JmolParser(source); + } + else + { + StructureImportSettings.setShowSeqFeatures(true); + return new MCview.PDBfile( + StructureImportSettings.isVisibleChainAnnotation(), + StructureImportSettings.isProcessSecondaryStructure(), + StructureImportSettings.isExternalSecondaryStructure(), + source); + } + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new JmolParser(); // todo or null? + } + }, + MMCif("mmCIF", "cif", true, false) + { + + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { - return new JmolParser( - StructureImportSettings.isVisibleChainAnnotation(), - StructureImportSettings.isProcessSecondaryStructure(), - StructureImportSettings.isExternalSecondaryStructure(), - inFile, sourceType); ++ return new JmolParser(inFile, sourceType); + } + + @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { - return new JmolParser( - StructureImportSettings.isVisibleChainAnnotation(), - StructureImportSettings.isProcessSecondaryStructure(), - StructureImportSettings.isExternalSecondaryStructure(), - source); ++ return new JmolParser(source); + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return new JmolParser(); // todo or null? + } + }, + Jalview("Jalview", "jar,jvp", true, true) + { + + @Override + public AlignmentFileI getAlignmentFile(String inFile, + DataSourceType sourceType) throws IOException + { + return null; + } + + @Override + public AlignmentFileI getAlignmentFile(FileParse source) + throws IOException + { + return null; + } + + @Override + public AlignmentFileI getAlignmentFile(AlignmentI al) + { + return null; + } + + @Override + public boolean isTextFormat() + { + return false; + } + }; + + /** + * A lookup map of enums by upper-cased name + */ + private static Map names; + static + { + names = new HashMap(); + for (FileFormat format : FileFormat.values()) + { + names.put(format.toString().toUpperCase(), format); + } + } + + private boolean writable; + + private boolean readable; + + private String extensions; + + private String name; + + /** + * Answers a list of writeable file formats (as string, corresponding to the + * toString() and forName() methods) + * + * @return + */ + public static List getWritableFormats(boolean textOnly) + { + List l = new ArrayList(); + for (FileFormatI ff : values()) + { + if (ff.isWritable() && (!textOnly || ff.isTextFormat())) + { + l.add(ff.toString()); + } + } + return l; + } + + /** + * Answers a list of readable file formats (as string, corresponding to the + * toString() and forName() methods) + * + * @return + */ + public static List getReadableFormats() + { + List l = new ArrayList(); + for (FileFormatI ff : values()) + { + if (ff.isReadable()) + { + l.add(ff.toString()); + } + } + return l; + } + + @Override + public boolean isComplexAlignFile() + { + return false; + } + + /** + * Returns the file format with the given name, or null if format is null or + * invalid. Unlike valueOf(), this is not case-sensitive, to be kind to + * writers of javascript. + * + * @param format + * @return + */ + public static FileFormatI forName(String format) + { + // or could store format.getShortDescription().toUpperCase() + // in order to decouple 'given name' from enum name + return format == null ? null : names.get(format.toUpperCase()); + } + + @Override + public boolean isReadable() + { + return readable; + } + + @Override + public boolean isWritable() + { + return writable; + } + + /** + * Constructor + * + * @param shortName + * @param extensions + * comma-separated list of file extensions associated with the format + * @param isReadable + * @param isWritable + */ + private FileFormat(String shortName, String extensions, + boolean isReadable, boolean isWritable) + { + this.name = shortName; + this.extensions = extensions; + this.readable = isReadable; + this.writable = isWritable; + } + + @Override + public String getExtensions() + { + return extensions; + } + + @Override + public String toString() + { + return name; + } + + @Override + public AlignmentFileI getAlignmentFile() + { + return getAlignmentFile((AlignmentI) null); + } + + @Override + public boolean isTextFormat() + { + return true; + } +} diff --cc src/jalview/io/HTMLOutput.java index 2e4a781,d58bd67..381a40b --- a/src/jalview/io/HTMLOutput.java +++ b/src/jalview/io/HTMLOutput.java @@@ -1,304 -1,168 +1,147 @@@ --/* -- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) -- * Copyright (C) $$Year-Rel$$ The Jalview Authors -- * -- * This file is part of Jalview. -- * -- * Jalview is free software: you can redistribute it and/or -- * modify it under the terms of the GNU General Public License -- * as published by the Free Software Foundation, either version 3 -- * of the License, or (at your option) any later version. -- * -- * Jalview is distributed in the hope that it will be useful, but -- * WITHOUT ANY WARRANTY; without even the implied warranty -- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR -- * PURPOSE. See the GNU General Public License for more details. -- * -- * You should have received a copy of the GNU General Public License -- * along with Jalview. If not, see . -- * The Jalview Authors are detailed in the 'AUTHORS' file. -- */ package jalview.io; - import jalview.bin.Cache; - import jalview.datamodel.AlignmentI; - import jalview.datamodel.SequenceI; - import jalview.gui.AlignViewport; + import jalview.api.AlignExportSettingI; + import jalview.datamodel.AlignmentExportData; + import jalview.exceptions.NoFileSelectedException; import jalview.gui.AlignmentPanel; - import jalview.gui.FeatureRenderer; - import jalview.gui.SequenceRenderer; - import jalview.util.BrowserLauncher; - import jalview.util.ImageMaker; + import jalview.gui.IProgressIndicator; import jalview.util.MessageManager; - import java.awt.Color; - import java.awt.Font; - import java.io.FileWriter; - import java.io.PrintWriter; + import java.io.BufferedReader; + import java.io.File; + import java.io.IOException; + import java.io.InputStreamReader; + import java.net.URL; + import java.util.Objects; - public class HTMLOutput - + public abstract class HTMLOutput implements Runnable { - AlignViewport av; + protected AlignmentPanel ap; - SequenceRenderer sr; + protected long pSessionId; - jalview.renderer.seqfeatures.FeatureRenderer fr; + protected IProgressIndicator pIndicator; - Color color; + protected File generatedFile; - public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr, - FeatureRenderer fr1) + public HTMLOutput(AlignmentPanel ap) { - this.av = ap.av; - this.sr = sr; - - fr = new FeatureRenderer(ap); - fr.transferSettings(fr1); - - JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), ImageMaker.HTML_EXTENSION, - "HTML files", "HTML files"); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_as_html")); - chooser.setToolTipText(MessageManager.getString("action.save")); - - int value = chooser.showSaveDialog(null); - - if (value == JalviewFileChooser.APPROVE_OPTION) + if (ap != null) { - String choice = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", chooser - .getSelectedFile().getParent()); - - try - { - PrintWriter out = new PrintWriter(new FileWriter(choice)); - out.println(""); - out.println(""); - out.println(""); - - if (av.getWrapAlignment()) - { - drawWrappedAlignment(out); - } - else - { - drawUnwrappedAlignment(out); - } - - out.println("\n\n"); - out.close(); - BrowserLauncher.openURL("file:///" + choice); - } catch (Exception ex) - { - ex.printStackTrace(); - } + this.ap = ap; + this.pIndicator = ap.alignFrame; } } - void drawUnwrappedAlignment(PrintWriter out) + public String getBioJSONData() { - out.println("
\n"); - out.println("\n"); - - // //////////// - SequenceI seq; - AlignmentI alignment = av.getAlignment(); - - // draws the top row, the measure rule - out.println(""); - - int i = 0; + return getBioJSONData(null); + } - for (i = 10; i < (alignment.getWidth() - 10); i += 10) + public String getBioJSONData(AlignExportSettingI exportSettings) + { + if (!isEmbedData()) { - out.println(""); + return null; } - - out.println(""); - out.println(""); - - for (i = 0; i < alignment.getHeight(); i++) + if (exportSettings == null) { - seq = alignment.getSequenceAt(i); - - String id = seq.getDisplayId(av.getShowJVSuffix()); - - out.println(""); - - for (int res = 0; res < seq.getLength(); res++) + exportSettings = new AlignExportSettingI() { - if (!jalview.util.Comparison.isGap(seq.getCharAt(res))) + @Override + public boolean isExportHiddenSequences() { - color = sr.getResidueBoxColour(seq, res); + return true; + } - color = fr.findFeatureColour(color, seq, res); + @Override + public boolean isExportHiddenColumns() + { + return true; } - else + + @Override + public boolean isExportAnnotations() { - color = Color.white; + return true; } - if (color.getRGB() < -1) + @Override + public boolean isExportFeatures() { - out.println(""); + return true; } - else + + @Override + public boolean isExportGroups() { - out.println(""); + return true; } - } - out.println(""); + @Override + public boolean isCancelled() + { + return false; + } + }; } - - // //////////// - out.println("
" + i + "
|		" + i - + "
|
" + id + "  " - + seq.getCharAt(res) + "" + seq.getCharAt(res) + "
"); - out.println("
"); + AlignmentExportData exportData = jalview.gui.AlignFrame - .getAlignmentForExport(JSONFile.FILE_DESC, ++ .getAlignmentForExport(FileFormat.Json, + ap.getAlignViewport(), exportSettings); + String bioJSON = new FormatAdapter(ap, exportData.getSettings()) - .formatSequences(JSONFile.FILE_DESC, exportData.getAlignment(), ++ .formatSequences(FileFormat.Json, exportData.getAlignment(), + exportData.getOmitHidden(), exportData + .getStartEndPostions(), ap.getAlignViewport() + .getColumnSelection()); + return bioJSON; } - void drawWrappedAlignment(PrintWriter out) + /** + * Read a template file content as string + * + * @param file + * - the file to be read + * @return File content as String + * @throws IOException + */ + public static String readFileAsString(File file) throws IOException { - // ////////////////////////////////// - // / How many sequences and residues can we fit on a printable page? - AlignmentI al = av.getAlignment(); - SequenceI seq; - String r; - String g; - String b; - - out.println("
\n"); - out.println("\n"); - - for (int startRes = 0; startRes < al.getWidth(); startRes += av - .getWrappedWidth()) + InputStreamReader isReader = null; + BufferedReader buffReader = null; + StringBuilder sb = new StringBuilder(); + Objects.requireNonNull(file, "File must not be null!"); + @SuppressWarnings("deprecation") + URL url = file.toURL(); + if (url != null) { - int endRes = startRes + av.getWrappedWidth(); - - if (endRes > al.getWidth()) - { - endRes = al.getWidth(); - } - - if (av.getScaleAboveWrapped()) + try { - out.println(""); - - if (av.getScaleLeftWrapped()) + isReader = new InputStreamReader(url.openStream()); + buffReader = new BufferedReader(isReader); + String line; + String lineSeparator = System.getProperty("line.separator"); + while ((line = buffReader.readLine()) != null) { - out.println(""); + sb.append(line).append(lineSeparator); } - else - { - out.println(""); - } - - for (int i = startRes + 10; i < endRes; i += 10) - { - out.println(""); - } - - out.println(""); - } - - int startPos, endPos; - for (int s = 0; s < al.getHeight(); s++) + + } catch (Exception ex) { - out.println(""); - seq = al.getSequenceAt(s); - - startPos = seq.findPosition(startRes); - endPos = seq.findPosition(endRes) - 1; - - String id = seq.getDisplayId(av.getShowJVSuffix()); - - out.println(""); - - if (av.getScaleLeftWrapped()) - { - if (startPos > seq.getEnd() || endPos == 0) - { - out.println(""); - } - else - { - out.println(""); - } - } - - for (int res = startRes; res < endRes; res++) - { - if (!jalview.util.Comparison.isGap(seq.getCharAt(res))) - { - color = sr.getResidueBoxColour(seq, res); - - color = fr.findFeatureColour(color, seq, res); - } - else - { - color = Color.white; - } - - if (color.getRGB() < -1) - { - out.println(""); - } - else - { - out.println(""); - } - - } - - if (av.getScaleRightWrapped() - && endRes < startRes + av.getWrappedWidth()) + ex.printStackTrace(); + } finally + { + if (isReader != null) { - out.println(""); + isReader.close(); } - - if (av.getScaleRightWrapped() && startPos < endPos) + + if (buffReader != null) { - out.println(""); + buffReader.close(); } - - out.println(""); - } - - if (endRes < al.getWidth()) - { - out.println(""); } } - - out.println("
  " + i + "
|
" + id + "   " + startPos + "  " - + seq.getCharAt(res) + "" + seq.getCharAt(res) + "" - + "   " + endPos + "  
"); - out.println("
"); + return sb.toString(); } public static String getImageMapHTML() @@@ -388,4 -252,122 +231,122 @@@ + "initToolTips(); //-->\n"); } - } + + public String getOutputFile() throws NoFileSelectedException + { + String selectedFile = null; + if (pIndicator != null && !isHeadless()) + { + pIndicator.setProgressBar(MessageManager.formatMessage( + "status.waiting_for_user_to_select_output_file", "HTML"), + pSessionId); + } + + JalviewFileChooser jvFileChooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[] { "html" }, new String[] { "HTML files" }, + "HTML files"); + jvFileChooser.setFileView(new JalviewFileView()); + + jvFileChooser.setDialogTitle(MessageManager + .getString("label.save_as_html")); + jvFileChooser.setToolTipText(MessageManager.getString("action.save")); + + int fileChooserOpt = jvFileChooser.showSaveDialog(null); + if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION) + { + jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser + .getSelectedFile().getParent()); + selectedFile = jvFileChooser.getSelectedFile().getPath(); + } + else + { + throw new NoFileSelectedException("No file was selected."); + } + return selectedFile; + } + + protected void setProgressMessage(String message) + { + if (pIndicator != null && !isHeadless()) + { + pIndicator.setProgressBar(message, pSessionId); + } + else + { + System.out.println(message); + } + } + + /** + * Answers true if HTML export is invoke in headless mode or false otherwise + * + * @return + */ + protected boolean isHeadless() + { + return System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true"); + } + + /** + * This method provides implementation of consistent behaviour which should + * occur before a HTML file export. It MUST be called at the start of the + * exportHTML() method implementation. + */ + protected void exportStarted() + { + pSessionId = System.currentTimeMillis(); + } + + /** + * This method provides implementation of consistent behaviour which should + * occur after a HTML file export. It MUST be called at the end of the + * exportHTML() method implementation. + */ + protected void exportCompleted() + { + if (isLaunchInBrowserAfterExport() && !isHeadless()) + { + try + { + jalview.util.BrowserLauncher + .openURL("file:///" + getExportedFile()); + } catch (IOException e) + { + e.printStackTrace(); + } + } + } + + /** + * if this answers true then BioJSON data will be embedded to the exported + * HTML file otherwise it won't be embedded. + * + * @return + */ + public abstract boolean isEmbedData(); + + /** + * if this answers true then the generated HTML file is opened for viewing in + * a browser after its generation otherwise it won't be opened in a browser + * + * @return + */ + public abstract boolean isLaunchInBrowserAfterExport(); + + /** + * handle to the generated HTML file + * + * @return + */ + public abstract File getExportedFile(); + + /** + * This is the main method to handle the HTML generation. + * + * @param outputFile + * the file path of the generated HTML + */ + public abstract void exportHTML(String outputFile); -} ++} diff --cc src/jalview/io/JalviewFileView.java index 4cef26d,4cef26d..c42771d --- a/src/jalview/io/JalviewFileView.java +++ b/src/jalview/io/JalviewFileView.java @@@ -53,6 -53,6 +53,7 @@@ public class JalviewFileView extends Fi alignSuffix.put("sto", "Stockholm File"); } ++ @Override public String getTypeDescription(File f) { String extension = getExtension(f); @@@ -69,6 -69,6 +70,7 @@@ return type; } ++ @Override public Icon getIcon(File f) { String extension = getExtension(f); diff --cc src/jalview/io/StructureFile.java index 152a2c0,97b246f..d39ab38 --- a/src/jalview/io/StructureFile.java +++ b/src/jalview/io/StructureFile.java @@@ -48,10 -72,11 +72,12 @@@ public abstract class StructureFile ext private Vector chains; + private boolean pdbIdAvailable; + - public StructureFile(String inFile, String type) throws IOException + public StructureFile(String inFile, DataSourceType sourceType) + throws IOException { - super(inFile, type); + super(inFile, sourceType); } public StructureFile(FileParse fp) throws IOException @@@ -264,11 -309,10 +310,8 @@@ Class cl = Class.forName("jalview.ext.jmol.JmolParser"); if (cl != null) { - final Constructor constructor = cl.getConstructor(new Class[] { - boolean.class, boolean.class, boolean.class, FileParse.class }); - final Object[] args = new Object[] { visibleChainAnnotation, - predictSecondaryStructure, externalSecondaryStructure, - new FileParse(getDataName(), dataSourceType) }; - final Constructor constructor = cl - .getConstructor(new Class[] { FileParse.class }); - final Object[] args = new Object[] { new FileParse(getDataName(), - type) }; ++ final Constructor constructor = cl.getConstructor(new Class[] {FileParse.class }); ++ final Object[] args = new Object[] { new FileParse(getDataName(), dataSourceType) }; StructureImportSettings.setShowSeqFeatures(false); StructureImportSettings.setVisibleChainAnnotation(false); diff --cc src/jalview/structure/StructureSelectionManager.java index 1738f99,b3968a3..65fd5e7 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@@ -322,12 -323,11 +323,11 @@@ public class StructureSelectionManage * @return null or the structure data parsed as a pdb file */ synchronized public StructureFile setMapping(SequenceI[] sequence, - String[] targetChains, String pdbFile, DataSourceType paste) - String[] targetChains, String pdbFile, String protocol) ++ String[] targetChains, String pdbFile, DataSourceType protocol) { - return setMapping(true, sequence, targetChains, pdbFile, paste); + return setMapping(true, sequence, targetChains, pdbFile, protocol); } - /** * create sequence structure mappings between each sequence and the given * pdbFile (retrieved via the given protocol). @@@ -348,8 -348,7 +348,7 @@@ */ synchronized public StructureFile setMapping(boolean forStructureView, SequenceI[] sequenceArray, String[] targetChainIds, - String pdbFile, - DataSourceType sourceType) - String pdbFile, String protocol) ++ String pdbFile, DataSourceType sourceType) { /* * There will be better ways of doing this in the future, for now we'll use @@@ -385,24 -384,10 +384,10 @@@ boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); try { - - boolean isParseWithJMOL = StructureImportSettings - .getDefaultPDBFileParser().equalsIgnoreCase( - StructureImportSettings.StructureParser.JMOL_PARSER - .toString()); - if (isParseWithJMOL || (pdbFile != null && isCIFFile(pdbFile))) - { - pdb = new JmolParser(addTempFacAnnot, parseSecStr, - secStructServices, pdbFile, sourceType); - } - else - { - pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, - pdbFile, sourceType); - } - pdb = new JmolParser(pdbFile, protocol); ++ pdb = new JmolParser(pdbFile, sourceType); if (pdb.getId() != null && pdb.getId().trim().length() > 0 - && sourceType == DataSourceType.FILE) - && AppletFormatAdapter.FILE.equals(protocol)) ++ && DataSourceType.FILE == sourceType) { registerPDBFile(pdb.getId().trim(), pdbFile); } @@@ -502,8 -496,8 +496,8 @@@ pdbFile = "INLINE" + pdb.getId(); } -- ArrayList seqToStrucMapping = new ArrayList(); - if (isMapUsingSIFTs) ++ List seqToStrucMapping = new ArrayList(); + if (isMapUsingSIFTs && seq.isProtein()) { setProgressBar(null); setProgressBar(MessageManager @@@ -532,7 -534,7 +534,7 @@@ } else { -- ArrayList foundSiftsMappings = new ArrayList(); ++ List foundSiftsMappings = new ArrayList(); for (PDBChain chain : pdb.getChains()) { try diff --cc src/jalview/structures/models/AAStructureBindingModel.java index 70fe609,5dc3465..6846de0 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@@ -124,11 -132,11 +133,11 @@@ public abstract class AAStructureBindin * @param pdbentry * @param sequenceIs * @param chains - * @param protocol2 + * @param protocol */ public AAStructureBindingModel(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, - DataSourceType protocol2) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, - String protocol) ++ DataSourceType protocol) { this.ssm = ssm; this.sequence = sequenceIs; diff --cc src/jalview/ws/dbsources/Pfam.java index 5b8a3ae,9acaa96..941bf1a --- a/src/jalview/ws/dbsources/Pfam.java +++ b/src/jalview/ws/dbsources/Pfam.java @@@ -121,14 -119,13 +121,13 @@@ abstract public class Pfam extends Xfa // retrieved. startQuery(); AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL() - + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL, - "STH"); + + queries.trim().toUpperCase(), DataSourceType.URL, + FileFormat.Stockholm); for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++) { - rcds.getSequenceAt(s).addDBRef( - new DBRefEntry(DBRefSource.PFAM, - // getDbSource(), - getDbVersion(), queries.trim().toUpperCase())); + rcds.getSequenceAt(s).addDBRef(new DBRefEntry(DBRefSource.PFAM, + // getDbSource(), + getDbVersion(), queries.trim().toUpperCase())); if (!getDbSource().equals(DBRefSource.PFAM)) { // add the specific ref too rcds.getSequenceAt(s).addDBRef( diff --cc test/MCview/PDBfileTest.java index 54576c6,2863643..a5bbf8e --- a/test/MCview/PDBfileTest.java +++ b/test/MCview/PDBfileTest.java @@@ -32,7 -33,8 +33,8 @@@ import jalview.datamodel.AlignmentI import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; -import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; + import jalview.structure.StructureImportSettings; import java.io.IOException; import java.util.List; @@@ -307,4 -310,19 +310,17 @@@ public class PDBfileTes pf.addAnnotations(al); return al.getAlignmentAnnotation(); } + - // @formatter:on - + @BeforeMethod(alwaysRun = true) + public void setUp() + { + Cache.loadProperties("test/jalview/io/testProps.jvprops"); + Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("ADD_SS_ANN", + Boolean.TRUE.toString()); + StructureImportSettings.setDefaultStructureFileFormat("PDB"); + } } diff --cc test/jalview/analysis/FinderTest.java index 0000000,91ceb82..4fdafde mode 000000,100644..100644 --- a/test/jalview/analysis/FinderTest.java +++ b/test/jalview/analysis/FinderTest.java @@@ -1,0 -1,309 +1,309 @@@ + /* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ + package jalview.analysis; + + import static org.testng.Assert.assertEquals; + import static org.testng.Assert.assertSame; + import static org.testng.Assert.assertTrue; + + import jalview.datamodel.Alignment; + import jalview.datamodel.AlignmentI; + import jalview.datamodel.SearchResultMatchI; + import jalview.datamodel.SearchResultsI; + import jalview.datamodel.Sequence; + import jalview.gui.AlignFrame; ++import jalview.io.DataSourceType; + import jalview.io.FileLoader; -import jalview.io.FormatAdapter; + + import java.util.List; + + import org.testng.annotations.BeforeClass; + import org.testng.annotations.Test; + + public class FinderTest + { + private AlignFrame af; + + private AlignmentI al; + + @BeforeClass(groups = "Functional") + public void setUp() + { + String seqData = "seq1 ABCD--EF-GHI\n" + "seq2 A--BCDefHI\n" + + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n"; + af = new FileLoader().LoadFileWaitTillLoaded(seqData, - FormatAdapter.PASTE); ++ DataSourceType.PASTE); + al = af.getViewport().getAlignment(); + } + + /** + * Test for find all matches of a regular expression + */ + @Test(groups = "Functional") + public void testFindAll_regex() + { + Finder f = new Finder(al, null); + f.setFindAll(true); + f.find("E.H"); // 'E, any character, H' + + // should match seq2 efH and seq3 EFH + SearchResultsI sr = f.getSearchResults(); + assertEquals(sr.getSize(), 2); + List matches = sr.getResults(); + assertSame(al.getSequenceAt(1), matches.get(0).getSequence()); + assertSame(al.getSequenceAt(2), matches.get(1).getSequence()); + assertEquals(matches.get(0).getStart(), 5); + assertEquals(matches.get(0).getEnd(), 7); + assertEquals(matches.get(1).getStart(), 4); + assertEquals(matches.get(1).getEnd(), 6); + } + + /** + * Test for (undocumented) find residue by position + */ + @Test(groups = "Functional") + public void testFind_residueNumber() + { + Finder f = new Finder(al, null); + f.setFindAll(true); + f.find("9"); + + // seq1 and seq4 have 9 residues; no match in other sequences + SearchResultsI sr = f.getSearchResults(); + assertEquals(sr.getSize(), 2); + List matches = sr.getResults(); + assertSame(al.getSequenceAt(0), matches.get(0).getSequence()); + assertSame(al.getSequenceAt(3), matches.get(1).getSequence()); + assertEquals(matches.get(0).getStart(), 9); + assertEquals(matches.get(0).getEnd(), 9); + assertEquals(matches.get(1).getStart(), 9); + assertEquals(matches.get(1).getEnd(), 9); + } + + /** + * Test for find next action + */ + @Test(groups = "Functional") + public void testFindNext() + { + /* + * start at second sequence; resIndex of -1 + * means sequence id / description is searched + */ + Finder f = new Finder(al, null, 1, -1); + f.find("e"); // matches id + + assertTrue(f.getSearchResults().isEmpty()); + assertEquals(f.getIdMatch().size(), 1); + assertSame(f.getIdMatch().get(0), al.getSequenceAt(1)); + + // resIndex is now 0 - for use in next find next + assertEquals(f.getResIndex(), 0); + f = new Finder(al, null, 1, 0); + f.find("e"); // matches in sequence + assertTrue(f.getIdMatch().isEmpty()); + assertEquals(f.getSearchResults().getSize(), 1); + List matches = f.getSearchResults().getResults(); + assertEquals(matches.get(0).getStart(), 5); + assertEquals(matches.get(0).getEnd(), 5); + assertSame(matches.get(0).getSequence(), al.getSequenceAt(1)); + // still in the second sequence + assertEquals(f.getSeqIndex(), 1); + // next residue position to search from is 5 + // (used as base 0 by RegEx so the same as 6 if base 1) + assertEquals(f.getResIndex(), 5); + + // find next from end of sequence - finds next sequence id + f = new Finder(al, null, 1, 5); + f.find("e"); + assertEquals(f.getIdMatch().size(), 1); + assertSame(f.getIdMatch().get(0), al.getSequenceAt(2)); + } + + /** + * Test for matching within sequence descriptions + */ + @Test(groups = "Functional") + public void testFindAll_inDescription() + { + AlignmentI al2 = new Alignment(al); + al2.getSequenceAt(0).setDescription("BRAF"); + al2.getSequenceAt(1).setDescription("braf"); + Finder f = new Finder(al2, null); + f.setFindAll(true); + f.setIncludeDescription(true); + + f.find("rAF"); + assertEquals(f.getIdMatch().size(), 2); + assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); + assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1)); + assertTrue(f.getSearchResults().isEmpty()); + + /* + * case sensitive + */ + f = new Finder(al2, null); + f.setFindAll(true); + f.setCaseSensitive(true); + f.setIncludeDescription(true); + + f.find("RAF"); + assertEquals(f.getIdMatch().size(), 1); + assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); + assertTrue(f.getSearchResults().isEmpty()); + + /* + * match sequence id, description and sequence! + */ + al2.getSequenceAt(0).setDescription("the efh sequence"); + al2.getSequenceAt(0).setName("mouseEFHkinase"); + al2.getSequenceAt(1).setName("humanEFHkinase"); + f = new Finder(al2, null); + f.setFindAll(true); + f.setIncludeDescription(true); + + /* + * sequence matches should have no duplicates + */ + f.find("EFH"); + assertEquals(f.getIdMatch().size(), 2); + assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); + assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1)); + + assertEquals(f.getSearchResults().getSize(), 2); + SearchResultMatchI match = f.getSearchResults().getResults().get(0); + assertSame(al2.getSequenceAt(1), match.getSequence()); + assertEquals(5, match.getStart()); + assertEquals(7, match.getEnd()); + match = f.getSearchResults().getResults().get(1); + assertSame(al2.getSequenceAt(2), match.getSequence()); + assertEquals(4, match.getStart()); + assertEquals(6, match.getEnd()); + } + + /** + * Test for matching within sequence ids + */ + @Test(groups = "Functional") + public void testFindAll_sequenceIds() + { + Finder f = new Finder(al, null); + f.setFindAll(true); + + /* + * case insensitive + */ + f.find("SEQ1"); + assertEquals(f.getIdMatch().size(), 1); + assertSame(f.getIdMatch().get(0), al.getSequenceAt(0)); + assertTrue(f.getSearchResults().isEmpty()); + + /* + * case sensitive + */ + f = new Finder(al, null); + f.setFindAll(true); + f.setCaseSensitive(true); + f.find("SEQ1"); + assertTrue(f.getSearchResults().isEmpty()); + + /* + * match both sequence id and sequence + */ + AlignmentI al2 = new Alignment(al); + al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ")); + f = new Finder(al2, null); + f.setFindAll(true); + f.find("ABZ"); + assertEquals(f.getIdMatch().size(), 1); + assertSame(f.getIdMatch().get(0), al2.getSequenceAt(4)); + assertEquals(f.getSearchResults().getSize(), 2); + SearchResultMatchI match = f.getSearchResults().getResults().get(0); + assertSame(al2.getSequenceAt(4), match.getSequence()); + assertEquals(4, match.getStart()); + assertEquals(6, match.getEnd()); + match = f.getSearchResults().getResults().get(1); + assertSame(al2.getSequenceAt(4), match.getSequence()); + assertEquals(10, match.getStart()); + assertEquals(12, match.getEnd()); + } + + /** + * Test finding all matches of a sequence pattern in an alignment + */ + @Test(groups = "Functional") + public void testFindAll_simpleMatch() + { + Finder f = new Finder(al, null); + f.setFindAll(true); + + /* + * case insensitive first + */ + f.find("EfH"); + SearchResultsI searchResults = f.getSearchResults(); + assertEquals(searchResults.getSize(), 2); + SearchResultMatchI match = searchResults.getResults().get(0); + assertSame(al.getSequenceAt(1), match.getSequence()); + assertEquals(5, match.getStart()); + assertEquals(7, match.getEnd()); + match = searchResults.getResults().get(1); + assertSame(al.getSequenceAt(2), match.getSequence()); + assertEquals(4, match.getStart()); + assertEquals(6, match.getEnd()); + + /* + * case sensitive + */ + f = new Finder(al, null); + f.setFindAll(true); + f.setCaseSensitive(true); + f.find("BC"); + searchResults = f.getSearchResults(); + assertEquals(searchResults.getSize(), 2); + match = searchResults.getResults().get(0); + assertSame(al.getSequenceAt(0), match.getSequence()); + assertEquals(2, match.getStart()); + assertEquals(3, match.getEnd()); + match = searchResults.getResults().get(1); + assertSame(al.getSequenceAt(1), match.getSequence()); + assertEquals(2, match.getStart()); + assertEquals(3, match.getEnd()); + } + + /** + * Test for JAL-2302 to verify that sub-matches are not included in a find all + * result + */ + @Test(groups = "Functional") + public void testFind_maximalResultOnly() + { + Finder f = new Finder(al, null); + f.setFindAll(true); + f.find("M+"); + SearchResultsI searchResults = f.getSearchResults(); + assertEquals(searchResults.getSize(), 1); + SearchResultMatchI match = searchResults.getResults().get(0); + assertSame(al.getSequenceAt(3), match.getSequence()); + assertEquals(4, match.getStart()); // dataset sequence positions + assertEquals(8, match.getEnd()); // base 1 + } + } diff --cc test/jalview/analysis/scoremodels/FeatureScoreModelTest.java index 1a95081,292b576..59985f3 --- a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java +++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java @@@ -24,9 -24,11 +24,11 @@@ import jalview.datamodel.AlignmentI import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; +import jalview.io.DataSourceType; import jalview.io.FileLoader; -import jalview.io.FormatAdapter; + import java.util.Arrays; + import org.testng.Assert; import org.testng.annotations.Test; @@@ -135,4 -139,45 +139,45 @@@ public class FeatureScoreModelTes + "(" + s + ") should still be distinct from FER1_MAIZE (3)"); } } + + /** + * Check findFeatureAt doesn't return contact features except at contact + * points TODO:move to under the FeatureRendererModel test suite + */ + @Test(groups = { "Functional" }) + public void testFindFeatureAt_PointFeature() throws Exception + { + String alignment = "a CCCCCCGGGGGGCCCCCC\n" + "b CCCCCCGGGGGGCCCCCC\n" + + "c CCCCCCGGGGGGCCCCCC\n"; + AlignFrame af = new jalview.io.FileLoader(false) - .LoadFileWaitTillLoaded(alignment, FormatAdapter.PASTE); ++ .LoadFileWaitTillLoaded(alignment, DataSourceType.PASTE); + SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0); + SequenceFeature sf = null; + sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, ""); + aseq.addSequenceFeature(sf); + Assert.assertTrue(sf.isContactFeature()); + af.refreshFeatureUI(true); + af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond")); + Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes() + .size(), 1, "Should be just one feature type displayed"); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 1) + .size(), 0); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 2) + .size(), 1); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 3) + .size(), 0); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 4) + .size(), 0); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 5) + .size(), 1); + // step through and check for pointwise feature presence/absence + Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 6) + .size(), 0); + } + } diff --cc test/jalview/controller/AlignViewControllerTest.java index 3eefada,e2c2130..f037599 --- a/test/jalview/controller/AlignViewControllerTest.java +++ b/test/jalview/controller/AlignViewControllerTest.java @@@ -7,7 -31,11 +31,11 @@@ import jalview.datamodel.Sequence import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; + import jalview.gui.AlignFrame; ++import jalview.io.DataSourceType; + import jalview.io.FileLoader; -import jalview.io.FormatAdapter; + import java.util.Arrays; import java.util.BitSet; import org.testng.annotations.Test; @@@ -97,4 -152,53 +152,53 @@@ public class AlignViewControllerTes assertEquals(0, seqCount); assertEquals(0, bs.cardinality()); } + + /** + * shameless copy of test data from findFeature for testing mark columns from + * highlight + */ + @Test(groups = "Functional") + public void testSelectColumnsWithHighlight() + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n" + + "seq3 aaaaaaaaaaMMMMMaaaaa\n" - + "seq4 aaaaaaaaaaaaaaaaaaaa\n", FormatAdapter.PASTE); ++ + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE); + + SearchResultsI sr = new SearchResults(); + SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); + SequenceI seq1 = sqs[0]; + SequenceI seq2 = sqs[1]; + SequenceI seq3 = sqs[2]; + SequenceI seq4 = sqs[3]; + + /* + * features start/end are base 1 + */ + sr.addResult(seq1, 2, 4); + sr.addResult(seq2, 4, 10); + sr.addResult(seq3, 11, 15); + + /* + * test Match/Find works first + */ + Finder f = new Finder(af.getViewport().getAlignment(), null); + f.setFindAll(true); + f.setCaseSensitive(true); + f.find("M+"); + assertEquals( + "Finder found different set of results to manually created SearchResults", + sr, f.getSearchResults()); + + /* + * now check simple mark columns from find operation + */ + af.getViewport().setSearchResults(sr); + AlignViewControllerI avc = af.avc; + + avc.markHighlightedColumns(false, false, false); + assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af + .getViewport().getColumnSelection().getSelectedRanges() + .toArray(), new int[][] { { 1, 14 } })); + } } diff --cc test/jalview/datamodel/AlignmentTest.java index 756bf71,7958e9b..42cdc8c --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@@ -27,9 -27,8 +27,10 @@@ import static org.testng.AssertJUnit.as import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; + import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; -import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; import jalview.io.FormatAdapter; import jalview.util.MapList; diff --cc test/jalview/ext/ensembl/EnsemblSeqProxyTest.java index b1ebdf8,d3a6e32..aee79fe --- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java +++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java @@@ -125,14 -144,13 +144,13 @@@ public class EnsemblSeqProxyTes } @Test(dataProvider = "ens_seqs", suiteName = "live") - public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq) - throws Exception + public void testGetOneSeqs(EnsemblRestClient proxy, String sq, + String fastasq) throws Exception { FileParse fp = proxy.getSequenceReader(Arrays - .asList(new String[] - { sq })); + .asList(new String[] { sq })); SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray(); - FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE); + FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE); SequenceI[] trueSqs = trueRes.getSeqsAsArray(); Assert.assertEquals(sqs.length, trueSqs.length, "Different number of sequences retrieved for query " + sq); diff --cc test/jalview/ext/jmol/JmolParserTest.java index f2b32c6,b2d3253..75b27c7 --- a/test/jalview/ext/jmol/JmolParserTest.java +++ b/test/jalview/ext/jmol/JmolParserTest.java @@@ -112,9 -117,8 +116,8 @@@ public class JmolParserTes for (String pdbStr : testFile) { PDBfile mctest = new PDBfile(false, false, false, pdbStr, - AppletFormatAdapter.FILE); - JmolParser jtest = new JmolParser(pdbStr, AppletFormatAdapter.FILE); + DataSourceType.FILE); - JmolParser jtest = new JmolParser(false, false, false, pdbStr, - DataSourceType.FILE); ++ JmolParser jtest = new JmolParser(pdbStr, DataSourceType.FILE); Vector seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs(); assertTrue( @@@ -179,13 -184,9 +183,8 @@@ public void testParse_missingResidues() throws Exception { PDBfile mctest = new PDBfile(false, false, false, - pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE); - JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak, - AppletFormatAdapter.PASTE); + pastePDBDataWithChainBreak, DataSourceType.PASTE); - boolean annotFromStructure = false; - boolean localSecondaryStruct = false; - boolean serviceSecondaryStruct = false; - JmolParser jtest = new JmolParser(annotFromStructure, - localSecondaryStruct, serviceSecondaryStruct, - pastePDBDataWithChainBreak, DataSourceType.PASTE); ++ JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak, DataSourceType.PASTE); Vector seqs = jtest.getSeqs(); Vector mcseqs = mctest.getSeqs(); @@@ -206,16 -207,12 +205,12 @@@ public void testParse_alternativeResidues() throws Exception { PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc, - AppletFormatAdapter.PASTE); + DataSourceType.PASTE); - boolean annotFromStructure = false; - boolean localSecondaryStruct = false; - boolean serviceSecondaryStruct = false; - JmolParser jtest = new JmolParser(annotFromStructure, - localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc, + JmolParser jtest = new JmolParser(pdbWithAltLoc, - AppletFormatAdapter.PASTE); + DataSourceType.PASTE); Vector seqs = jtest.getSeqs(); Vector mcseqs = mctest.getSeqs(); - + assertEquals("Failed to find 1 sequence\n", 1, seqs.size()); assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size()); assertEquals("ALC", seqs.get(0).getSequenceAsString()); @@@ -252,4 -249,30 +247,30 @@@ assertEquals('H', structCode[4]); assertEquals('E', structCode[5]); } + + @Test(groups = "Functional") + public void testLocalPDBId() throws Exception + { + JmolParser structureData; + /* + * reads a local structure + */ + structureData = new JmolParser("examples/testdata/localstruct.pdb", - AppletFormatAdapter.FILE); ++ DataSourceType.FILE); + assertNotNull(structureData); + /* + * local structure files should yield a false ID based on the filename + */ + assertNotNull(structureData.getId()); + assertEquals(structureData.getId(), "localstruct.pdb"); + assertNotNull(structureData.getSeqs()); + /* + * the ID is also the group for features derived from structure data + */ + assertNotNull(structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup); + assertEquals( + structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup, + "localstruct.pdb"); + + } } diff --cc test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java index 01b4adf,254e082..6baa1dd --- a/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java +++ b/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java @@@ -51,10 -71,9 +71,8 @@@ public class JmolVsJalviewPDBParserEndT JmolParser jtest = null; try { -- mctest = new PDBfile(false, false, false, testFile, - DataSourceType.FILE); - jtest = new JmolParser(false, false, false, testFile, - DataSourceType.FILE); - AppletFormatAdapter.FILE); - jtest = new JmolParser(testFile, AppletFormatAdapter.FILE); ++ mctest = new PDBfile(false, false, false, testFile, DataSourceType.FILE); ++ jtest = new JmolParser(testFile, DataSourceType.FILE); } catch (IOException e) { System.err.println("Exception thrown while parsing : " + pdbStr); diff --cc test/jalview/gui/AlignViewportTest.java index 8c540b0,dfe0e68..d6b2454 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@@ -26,15 -26,23 +26,23 @@@ import static org.testng.AssertJUnit.as import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; + import jalview.bin.Cache; + import jalview.bin.Jalview; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; + import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; + import jalview.datamodel.Annotation; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; + import jalview.datamodel.SearchResults; + import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; import jalview.io.FileLoader; -import jalview.io.FormatAdapter; + import jalview.schemes.ColourSchemeI; + import jalview.schemes.PIDColourScheme; import jalview.structure.StructureSelectionManager; import jalview.util.MapList; @@@ -296,4 -304,73 +304,73 @@@ public class AlignViewportTes assertTrue(ssmMappings.contains(acf2)); assertFalse(ssmMappings.contains(acf3)); } + + /** + * Test for JAL-1306 - conservation thread should run even when only Quality + * (and not Conservation) is enabled in Preferences + */ + @Test(groups = { "Functional" }) + public void testUpdateConservation_qualityOnly() + { + Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("SHOW_QUALITY", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("SHOW_CONSERVATION", + Boolean.FALSE.toString()); + Cache.applicationProperties.setProperty("SHOW_IDENTITY", + Boolean.FALSE.toString()); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/uniref50.fa", FormatAdapter.FILE); ++ "examples/uniref50.fa", DataSourceType.FILE); + AlignmentAnnotation[] anns = af.viewport.getAlignment() + .getAlignmentAnnotation(); + assertNotNull("No annotations found", anns); + assertEquals("More than one annotation found", 1, anns.length); + assertTrue("Annotation is not Quality", + anns[0].description.startsWith("Alignment Quality")); + Annotation[] annotations = anns[0].annotations; + assertNotNull("Quality annotations are null", annotations); + assertNotNull("Quality in column 1 is null", annotations[0]); + assertTrue("No quality value in column 1", annotations[0].value > 10f); + } + + @Test(groups = { "Functional" }) + public void testSetGlobalColourScheme() + { + /* + * test for JAL-2283 don't inadvertently turn on colour by conservation + */ + Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE"); + Cache.applicationProperties.setProperty("SHOW_CONSERVATION", + Boolean.TRUE.toString()); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/uniref50.fa", FormatAdapter.FILE); ++ "examples/uniref50.fa", DataSourceType.FILE); + ColourSchemeI cs = new PIDColourScheme(); + af.getViewport().setGlobalColourScheme(cs); + assertFalse(cs.conservationApplied()); + } + + @Test(groups = { "Functional" }) + public void testSetGetHasSearchResults() + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/uniref50.fa", FormatAdapter.FILE); ++ "examples/uniref50.fa", DataSourceType.FILE); + SearchResultsI sr = new SearchResults(); + SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0); + + // create arbitrary range on first sequence + sr.addResult(s1, s1.getStart() + 10, s1.getStart() + 15); + + // test set + af.getViewport().setSearchResults(sr); + // has -> true + assertTrue(af.getViewport().hasSearchResults()); + // get == original + assertEquals(sr, af.getViewport().getSearchResults()); + + // set(null) results in has -> false + + af.getViewport().setSearchResults(null); + assertFalse(af.getViewport().hasSearchResults()); + } } diff --cc test/jalview/gui/PopupMenuTest.java index 0ad75e8,14354ff..38c0de3 --- a/test/jalview/gui/PopupMenuTest.java +++ b/test/jalview/gui/PopupMenuTest.java @@@ -27,9 -29,11 +29,12 @@@ import static org.testng.AssertJUnit.as import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; + import jalview.datamodel.DBRefEntry; + import jalview.datamodel.DBRefSource; + import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; -import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; import jalview.io.FormatAdapter; import jalview.util.MessageManager; diff --cc test/jalview/io/CrossRef2xmlTests.java index 0000000,c55ddd9..070fa68 mode 000000,100644..100644 --- a/test/jalview/io/CrossRef2xmlTests.java +++ b/test/jalview/io/CrossRef2xmlTests.java @@@ -1,0 -1,573 +1,574 @@@ + /* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ + package jalview.io; + + import jalview.analysis.CrossRef; + import jalview.api.AlignmentViewPanel; + import jalview.datamodel.AlignedCodonFrame; + import jalview.datamodel.AlignmentI; + import jalview.datamodel.AlignmentTest; + import jalview.datamodel.SequenceI; + import jalview.gui.AlignFrame; + import jalview.gui.CrossRefAction; + import jalview.gui.Desktop; + import jalview.gui.Jalview2XML; + + import java.io.File; + import java.io.IOException; + import java.util.ArrayList; + import java.util.HashMap; + import java.util.List; + + import org.testng.Assert; + import org.testng.annotations.Test; + + @Test(singleThreaded = true) + public class CrossRef2xmlTests extends Jalview2xmlBase + { + + /** + * test store and recovery of all reachable cross refs from all reachable + * crossrefs for one or more fetched db refs. Currently, this test has a known + * failure case. + * + * @throws Exception + */ + @Test(groups = { "Operational" }, enabled = true) + public void testRetrieveAndShowCrossref() throws Exception + { + + List failedDBRetr = new ArrayList(); + List failedXrefMenuItems = new ArrayList(); + List failedProjectRecoveries = new ArrayList(); + + // for every set of db queries + // retrieve db query + // verify presence of expected xrefs + // show xrefs - verify expected type of frame is shown for each xref + // show xrefs again + // - verify original -> xref -> xref(original) recovers frame containing at + // least the first retrieved sequence + // store + // 1. whole project + // 2. individual frames + // 3. load each one back and verify + // . aligned sequences (.toString() ) + // . xrefs (.toString() ) + // . codonframes + // + // + HashMap dbtoviewBit = new HashMap(); + List keyseq = new ArrayList(); + HashMap savedProjects = new HashMap(); + + for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" }, + { "UNIPROT", "P01731" } }) + { + // pass counters - 0 - first pass, 1 means retrieve project rather than + // perform action + int pass1 = 0, pass2 = 0, pass3 = 0; + // each do loop performs two iterations in the first outer loop pass, but + // only performs one iteration on the second outer loop + // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1 + // { pass 2 = 0 { pass 3 = 0 } } + do + { + String first = did[0] + " " + did[1]; + AlignFrame af = null; + boolean dna; + AlignmentI retral; + AlignmentI dataset; + SequenceI[] seqs; + List ptypes = null; + if (pass1 == 0) + { + // retrieve dbref + + List afs = jalview.gui.SequenceFetcher.fetchAndShow( + did[0], did[1]); + if (afs.size() == 0) + { + failedDBRetr.add("Didn't retrieve " + first); + break; + } + keyseq.add(first); + af = afs.get(0); + + // verify references for retrieved data + AlignmentTest.assertAlignmentDatasetRefs(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Fetch " + first + ":"); + assertDatasetIsNormalisedKnownDefect(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Fetch " + first + ":"); + dna = af.getViewport().getAlignment().isNucleotide(); + retral = af.getViewport().getAlignment(); + dataset = retral.getDataset(); + seqs = retral.getSequencesArray(); + + } + else + { + Desktop.instance.closeAll_actionPerformed(null); + // recover stored project + af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects - .get(first).toString(), FormatAdapter.FILE); ++ .get(first).toString(), DataSourceType.FILE); + System.out.println("Recovered view for '" + first + "' from '" + + savedProjects.get(first).toString() + "'"); + dna = af.getViewport().getAlignment().isNucleotide(); + retral = af.getViewport().getAlignment(); + dataset = retral.getDataset(); + seqs = retral.getSequencesArray(); + + // verify references for recovered data + AlignmentTest.assertAlignmentDatasetRefs(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Recover " + first + ":"); + assertDatasetIsNormalisedKnownDefect(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Recover " + first + ":"); + + } + + // store project on first pass, compare next pass + stringify(dbtoviewBit, savedProjects, first, af.alignPanel); + + ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef( + seqs, dataset).findXrefSourcesForSequences(dna); + + // start of pass2: retrieve each cross-ref for fetched or restored + // project. + do // first cross ref and recover crossref loop + { + + for (String db : ptypes) + { + // counter for splitframe views retrieved via crossref + int firstcr_ap = 0; + // build next key so we an retrieve all views + String nextxref = first + " -> " + db + "{" + firstcr_ap + "}"; + // perform crossref action, or retrieve stored project + List cra_views = new ArrayList(); + CrossRefAction cra = null; + + if (pass2 == 0) + { // retrieve and show cross-refs in this thread + cra = new CrossRefAction(af, seqs, dna, db); + cra.run(); + if (cra.getXrefViews().size() == 0) + { + failedXrefMenuItems.add("No crossrefs retrieved for " + + first + " -> " + db); + continue; + } + cra_views = cra.getXrefViews(); + assertNucleotide(cra_views.get(0), + "Nucleotide panel included proteins for " + first + + " -> " + db); + assertProtein(cra_views.get(1), + "Protein panel included nucleotides for " + first + + " -> " + db); + } + else + { + Desktop.instance.closeAll_actionPerformed(null); + pass3 = 0; + // recover stored project + File storedProject = savedProjects.get(nextxref); + if (storedProject == null) + { + failedProjectRecoveries.add("Failed to store a view for '" + + nextxref + "'"); + continue; + } + + // recover stored project + AlignFrame af2 = new FileLoader(false) + .LoadFileWaitTillLoaded(savedProjects.get(nextxref) - .toString(), FormatAdapter.FILE); ++ .toString(), DataSourceType.FILE); + System.out.println("Recovered view for '" + nextxref + + "' from '" + savedProjects.get(nextxref).toString() + + "'"); + // gymnastics to recover the alignPanel/Complementary alignPanel + if (af2.getViewport().isNucleotide()) + { + // top view, then bottom + cra_views.add(af2.getViewport().getAlignPanel()); + cra_views.add(((jalview.gui.AlignViewport) af2 + .getViewport().getCodingComplement()) + .getAlignPanel()); + + } + else + { + // bottom view, then top + cra_views.add(((jalview.gui.AlignViewport) af2 + .getViewport().getCodingComplement()) + .getAlignPanel()); + cra_views.add(af2.getViewport().getAlignPanel()); + + } + } + HashMap> xrptypes = new HashMap>(); + // first save/verify views. + for (AlignmentViewPanel avp : cra_views) + { + nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}"; + // verify references for this panel + AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(), + "Pass (" + pass1 + "," + pass2 + "," + pass3 + + "): before start of pass3: " + nextxref + + ":"); + assertDatasetIsNormalisedKnownDefect(avp.getAlignment(), + "Pass (" + pass1 + "," + pass2 + "," + pass3 + + "): before start of pass3: " + nextxref + + ":"); + + SequenceI[] xrseqs = avp.getAlignment().getSequencesArray(); + + List _xrptypes = (seqs == null || seqs.length == 0) ? null + : new CrossRef(xrseqs, dataset) + .findXrefSourcesForSequences(avp + .getAlignViewport().isNucleotide()); + + stringify(dbtoviewBit, savedProjects, nextxref, avp); + xrptypes.put(nextxref, _xrptypes); + + } + + // now do the second xref pass starting from either saved or just + // recovered split pane, in sequence + do // retrieve second set of cross refs or recover and verify + { + firstcr_ap = 0; + for (AlignmentViewPanel avp : cra_views) + { + nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}"; + for (String xrefdb : xrptypes.get(nextxref)) + { + List cra_views2 = new ArrayList(); + int q = 0; + String nextnextxref = nextxref + " -> " + xrefdb + "{" + + q + "}"; + + if (pass3 == 0) + { + + SequenceI[] xrseqs = avp.getAlignment() + .getSequencesArray(); + AlignFrame nextaf = Desktop.getAlignFrameFor(avp + .getAlignViewport()); + + cra = new CrossRefAction(nextaf, xrseqs, avp + .getAlignViewport().isNucleotide(), xrefdb); + cra.run(); + if (cra.getXrefViews().size() == 0) + { + failedXrefMenuItems + .add("No crossrefs retrieved for '" + + nextxref + "' to " + xrefdb + + " via '" + nextaf.getTitle() + "'"); + continue; + } + cra_views2 = cra.getXrefViews(); + assertNucleotide(cra_views2.get(0), + "Nucleotide panel included proteins for '" + + nextxref + "' to " + xrefdb + + " via '" + nextaf.getTitle() + "'"); + assertProtein(cra_views2.get(1), + "Protein panel included nucleotides for '" + + nextxref + "' to " + xrefdb + + " via '" + nextaf.getTitle() + "'"); + + } + else + { + Desktop.instance.closeAll_actionPerformed(null); + // recover stored project + File storedProject = savedProjects.get(nextnextxref); + if (storedProject == null) + { + failedProjectRecoveries + .add("Failed to store a view for '" + + nextnextxref + "'"); + continue; + } + AlignFrame af2 = new FileLoader(false) + .LoadFileWaitTillLoaded( + savedProjects.get(nextnextxref) - .toString(), FormatAdapter.FILE); ++ .toString(), ++ DataSourceType.FILE); + System.out.println("Recovered view for '" + + nextnextxref + "' from '" + + savedProjects.get(nextnextxref).toString() + + "'"); + // gymnastics to recover the alignPanel/Complementary + // alignPanel + if (af2.getViewport().isNucleotide()) + { + // top view, then bottom + cra_views2.add(af2.getViewport().getAlignPanel()); + cra_views2.add(((jalview.gui.AlignViewport) af2 + .getViewport().getCodingComplement()) + .getAlignPanel()); + + } + else + { + // bottom view, then top + cra_views2.add(((jalview.gui.AlignViewport) af2 + .getViewport().getCodingComplement()) + .getAlignPanel()); + cra_views2.add(af2.getViewport().getAlignPanel()); + } + Assert.assertEquals(cra_views2.size(), 2); + Assert.assertNotNull(cra_views2.get(0)); + Assert.assertNotNull(cra_views2.get(1)); + } + + for (AlignmentViewPanel nextavp : cra_views2) + { + nextnextxref = nextxref + " -> " + xrefdb + "{" + q++ + + "}"; + + // verify references for this panel + AlignmentTest.assertAlignmentDatasetRefs( + nextavp.getAlignment(), "" + "Pass (" + pass1 + + "," + pass2 + "): For " + + nextnextxref + ":"); + assertDatasetIsNormalisedKnownDefect( + nextavp.getAlignment(), "" + "Pass (" + pass1 + + "," + pass2 + "): For " + + nextnextxref + ":"); + + stringify(dbtoviewBit, savedProjects, nextnextxref, + nextavp); + keyseq.add(nextnextxref); + } + } // end of loop around showing all xrefdb for crossrf2 + + } // end of loop around all viewpanels from crossrf1 + } while (pass2 == 2 && pass3++ < 2); + // fetchdb->crossref1->crossref-2->verify for xrefs we + // either loop twice when pass2=0, or just once when pass2=1 + // (recovered project from previous crossref) + + } // end of loop over db-xrefs for crossref-2 + + // fetchdb-->crossref1 + // for each xref we try to retrieve xref, store and verify when + // pass1=0, or just retrieve and verify when pass1=1 + } while (pass1 == 1 && pass2++ < 2); + // fetchdb + // for each ref we + // loop twice: first, do the retrieve, second recover from saved project + + // increment pass counters, so we repeat traversal starting from the + // oldest saved project first. + if (pass1 == 0) + { + // verify stored projects for first set of cross references + pass1 = 1; + // and verify cross-references retrieved from stored projects + pass2 = 0; + pass3 = 0; + } + else + { + pass1++; + } + } while (pass1 < 3); + } + if (failedXrefMenuItems.size() > 0) + { + for (String s : failedXrefMenuItems) + { + System.err.println(s); + } + Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size() + + " counts)"); + } + if (failedProjectRecoveries.size() > 0) + { + + for (String s : failedProjectRecoveries) + { + System.err.println(s); + } + Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) (" + + failedProjectRecoveries.size() + " counts)"); + } + if (failedDBRetr.size() > 0) + { + for (String s : failedProjectRecoveries) + { + System.err.println(s); + } + Assert.fail("Didn't retrieve some db refs for checking cross-refs (" + + failedDBRetr.size() + " counts)"); + } + } + + /** + * wrapper to trap known defect for AH002001 testcase + * + * @param alignment + * @param string + */ + private void assertDatasetIsNormalisedKnownDefect(AlignmentI al, + String message) + { + try + { + AlignmentTest.assertDatasetIsNormalised(al, message); + } catch (AssertionError ae) + { + if (!ae.getMessage().endsWith("EMBL|AH002001")) + { + throw ae; + } + else + { + System.out + .println("Ignored exception for known defect: JAL-2179 : " + + message); + } + + } + } + + private void assertProtein(AlignmentViewPanel alignmentViewPanel, + String message) + { + assertType(true, alignmentViewPanel, message); + } + + private void assertNucleotide(AlignmentViewPanel alignmentViewPanel, + String message) + { + assertType(false, alignmentViewPanel, message); + } + + private void assertType(boolean expectProtein, + AlignmentViewPanel alignmentViewPanel, String message) + { + List nonType = new ArrayList(); + for (SequenceI sq : alignmentViewPanel.getAlignViewport() + .getAlignment().getSequences()) + { + if (sq.isProtein() != expectProtein) + { + nonType.add(sq); + } + } + if (nonType.size() > 0) + { + Assert.fail(message + " [ " + + (expectProtein ? "nucleotides were " : "proteins were ") + + nonType.toString() + " ]"); + } + } + + /** + * first time called, record strings derived from alignment and + * alignedcodonframes, and save view to a project file. Second time called, + * compare strings to existing ones. org.testng.Assert.assertTrue on + * stringmatch + * + * @param dbtoviewBit + * map between xrefpath and view string + * @param savedProjects + * - map from xrefpath to saved project filename (createTempFile) + * @param xrefpath + * - xrefpath - unique ID for this context (composed of sequence of + * db-fetch/cross-ref actions preceeding state) + * @param avp + * - viewpanel to store (for viewpanels in splitframe, the same + * project should be written for both panels, only one needs + * recovering for comparison on the next stringify call, but each + * viewpanel needs to be called with a distinct xrefpath to ensure + * each one's strings are compared) + */ + private void stringify(HashMap dbtoviewBit, + HashMap savedProjects, String xrefpath, + AlignmentViewPanel avp) + { + if (savedProjects != null) + { + if (savedProjects.get(xrefpath) == null) + { + // write a project file for this view. On the second pass, this will be + // recovered and cross-references verified + try + { + File prfile = File.createTempFile("crossRefTest", ".jvp"); + AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport()); + new Jalview2XML(false).saveAlignment(af, prfile.toString(), + af.getTitle()); + System.out.println("Written view from '" + xrefpath + "' as '" + + prfile.getAbsolutePath() + "'"); + savedProjects.put(xrefpath, prfile); + } catch (IOException q) + { + Assert.fail("Unexpected IO Exception", q); + } + } + else + { + System.out.println("Stringify check on view from '" + xrefpath + + "' [ possibly retrieved from '" + + savedProjects.get(xrefpath).getAbsolutePath() + "' ]"); + + } + } + + StringBuilder sbr = new StringBuilder(); + sbr.append(avp.getAlignment().toString()); + sbr.append("\n"); + sbr.append(""); + sbr.append("\n"); + sbr.append(avp.getAlignment().getDataset()); + sbr.append("\n"); + sbr.append(""); + sbr.append("\n"); + int p = 0; + if (avp.getAlignment().getCodonFrames() != null) + { + for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames()) + { + sbr.append(""); + sbr.append("\n"); + sbr.append(ac.toString()); + sbr.append("\n"); + } + } + String dbt = dbtoviewBit.get(xrefpath); + if (dbt == null) + { + dbtoviewBit.put(xrefpath, sbr.toString()); + } + else + { + Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for " + + xrefpath); + } + } + } diff --cc test/jalview/io/Jalview2xmlTests.java index 266b0f8,3d53234..b6f29ae --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@@ -119,9 -68,9 +68,9 @@@ public class Jalview2xmlTests extends J String inFile = "examples/RF00031_folded.stk"; String tfile = File.createTempFile("JalviewTest", ".jvp") .getAbsolutePath(); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, - FormatAdapter.FILE); - assertNotNull("Didn't read input file " + inFile, af); ++ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + inFile, DataSourceType.FILE); + assertTrue("Didn't read input file " + inFile, af != null); int olddsann = countDsAnn(af.getViewport()); assertTrue("Didn't find any dataset annotations", olddsann > 0); af.rnahelicesColour_actionPerformed(null); @@@ -129,12 -78,11 +78,11 @@@ "Couldn't apply RNA helices colourscheme", af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); assertTrue("Failed to store as a project.", - af.saveAlignment(tfile, "Jalview")); + af.saveAlignment(tfile, FileFormat.Jalview)); af.closeMenuItem_actionPerformed(true); af = null; - af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, - DataSourceType.FILE); - af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE); - assertNotNull("Failed to import new project", af); ++ af = new FileLoader().LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); + assertTrue("Failed to import new project", af != null); int newdsann = countDsAnn(af.getViewport()); assertTrue( "Differing numbers of dataset sequence annotation\nOriginally " @@@ -154,32 -102,26 +102,27 @@@ String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii"; String tfile = File.createTempFile("JalviewTest", ".jvp") .getAbsolutePath(); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, - FormatAdapter.FILE); ++ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + inFile, DataSourceType.FILE); - assertTrue("Didn't read input file " + inFile, af != null); + assertNotNull("Didn't read input file " + inFile, af); - af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null); + af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); - assertTrue( - "Didn't set T-coffee colourscheme", - af.getViewport().getGlobalColourScheme().getClass() - .equals(jalview.schemes.TCoffeeColourScheme.class)); - assertTrue( - "Recognise T-Coffee score from string", - jalview.schemes.ColourSchemeProperty.getColour(af.getViewport() - .getAlignment(), - jalview.schemes.ColourSchemeProperty.getColourName(af - .getViewport().getGlobalColourScheme())) != null); + assertSame("Didn't set T-coffee colourscheme", af.getViewport() + .getGlobalColourScheme().getClass(), TCoffeeColourScheme.class); + assertNotNull("Recognise T-Coffee score from string", - jalview.schemes.ColourSchemeProperty.getColour(af.getViewport() ++ ColourSchemeProperty.getColour(af.getViewport() + .getAlignment(), ColourSchemeProperty.getColourName(af + .getViewport().getGlobalColourScheme()))); assertTrue("Failed to store as a project.", - af.saveAlignment(tfile, "Jalview")); + af.saveAlignment(tfile, FileFormat.Jalview)); af.closeMenuItem_actionPerformed(true); af = null; - af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, - af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE); ++ af = new FileLoader().LoadFileWaitTillLoaded(tfile, + DataSourceType.FILE); - assertTrue("Failed to import new project", af != null); - assertTrue( - "Didn't set T-coffee colourscheme for imported project.", - af.getViewport().getGlobalColourScheme().getClass() - .equals(jalview.schemes.TCoffeeColourScheme.class)); + assertNotNull("Failed to import new project", af); + assertSame("Didn't set T-coffee colourscheme for imported project.", af + .getViewport().getGlobalColourScheme().getClass(), + TCoffeeColourScheme.class); System.out .println("T-Coffee score shading successfully recovered from project."); } @@@ -190,10 -132,10 +133,9 @@@ String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva"; String tfile = File.createTempFile("JalviewTest", ".jvp") .getAbsolutePath(); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - inFile, DataSourceType.FILE); - assertTrue("Didn't read input file " + inFile, af != null); - AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, - FormatAdapter.FILE); ++ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, DataSourceType.FILE); + assertNotNull("Didn't read input file " + inFile, af); - af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null); + af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); AlignmentAnnotation[] aa = af.getViewport().getAlignment() .getSequenceAt(0).getAnnotation("IUPredWS (Short)"); assertTrue( @@@ -215,12 -157,11 +157,11 @@@ sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true); af.alignPanel.alignmentChanged(); assertTrue("Failed to store as a project.", - af.saveAlignment(tfile, "Jalview")); + af.saveAlignment(tfile, FileFormat.Jalview)); af.closeMenuItem_actionPerformed(true); af = null; - af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, - DataSourceType.FILE); - af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE); - assertNotNull("Failed to import new project", af); ++ af = new FileLoader().LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); + assertTrue("Failed to import new project", af != null); // check for group and alignment colourschemes @@@ -275,9 -216,9 +216,9 @@@ { int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop .getAlignFrames().length; - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); + "examples/exampleFile_2_7.jar", DataSourceType.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); assertTrue("Didn't gather the views in the example file.", Desktop.getAlignFrames().length == 1 + origCount); @@@ -286,14 -227,11 +227,11 @@@ @Test(groups = { "Functional" }) public void viewRefPdbAnnotation() throws Exception { - // TODO: Make this pass without setting StructureParser.JALVIEW_PARSER - // StructureImportSettings - // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER); StructureImportSettings.setProcessSecondaryStructure(true); StructureImportSettings.setVisibleChainAnnotation(true); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); + "examples/exampleFile_2_7.jar", DataSourceType.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); AlignmentViewPanel sps = null; for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) { @@@ -350,9 -290,9 +290,9 @@@ @Test(groups = { "Functional" }) public void testCopyViewSettings() throws Exception { - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); + "examples/exampleFile_2_7.jar", DataSourceType.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); AlignmentViewPanel sps = null, groups = null; for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) { @@@ -390,9 -330,8 +330,8 @@@ { Desktop.instance.closeAll_actionPerformed(null); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); + "examples/exampleFile_2_7.jar", DataSourceType.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); Assert.assertEquals(Desktop.getAlignFrames().length, 1); String afid = af.getViewport().getSequenceSetId(); @@@ -423,8 -362,8 +362,8 @@@ { Assert.assertEquals(Desktop.getAlignFrames().length, 0); } - af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), - FormatAdapter.FILE); ++ af = new FileLoader().LoadFileWaitTillLoaded( + tfile.getAbsolutePath(), DataSourceType.FILE); Assert.assertNotNull(af); Assert.assertEquals( Desktop.getAlignFrames().length, @@@ -445,8 -384,8 +384,8 @@@ { Desktop.instance.closeAll_actionPerformed(null); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); + "examples/exampleFile_2_7.jar", DataSourceType.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); String afid = af.getViewport().getSequenceSetId(); // remember reference sequence for each panel @@@ -578,8 -517,8 +517,8 @@@ { Desktop.instance.closeAll_actionPerformed(null); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - "examples/uniref50.fa", FormatAdapter.FILE); + "examples/uniref50.fa", DataSourceType.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); String afid = af.getViewport().getSequenceSetId(); // make a second view of the alignment af.newView_actionPerformed(null); @@@ -656,11 -595,11 +595,11 @@@ { Assert.assertEquals(Desktop.getAlignFrames().length, 0); } - - af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), - FormatAdapter.FILE); + + af = new FileLoader().LoadFileWaitTillLoaded( + tfile.getAbsolutePath(), DataSourceType.FILE); afid = af.getViewport().getSequenceSetId(); - + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) { String viewName = ap.getViewName(); @@@ -700,8 -638,8 +638,8 @@@ Desktop.instance.closeAll_actionPerformed(null); String exampleFile = "examples/3W5V.pdb"; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile, - FormatAdapter.FILE); + DataSourceType.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); String afid = af.getViewport().getSequenceSetId(); AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid); diff --cc test/jalview/io/PfamFormatInputTest.java index 8eb3c60,fb99865..f0986af --- a/test/jalview/io/PfamFormatInputTest.java +++ b/test/jalview/io/PfamFormatInputTest.java @@@ -9,24 -29,22 +29,22 @@@ import org.testng.annotations.Test public class PfamFormatInputTest { - @Test + @Test(groups = "Functional") public void testPfamFormatNoLimits() throws IOException { - AlignmentI al = new jalview.io.AppletFormatAdapter().readFile("ASEQ" + AlignmentI al = new AppletFormatAdapter().readFile("ASEQ" - + '\t' + "...--FFAFAFF--", AppletFormatAdapter.PASTE, "PFAM"); + + '\t' + "...--FFAFAFF--", DataSourceType.PASTE, + FileFormat.Pfam); Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences"); Assert.assertTrue(al.hasValidSequence(), "Didn't extract limits from PFAM ID"); } - @Test + @Test(groups = "Functional") public void testPfamFormatValidLimits() throws IOException { - AlignmentI al = new jalview.io.AppletFormatAdapter().readFile( - "ASEQ/15-25" + '\t' + "...--FFAFAFF--", - DataSourceType.PASTE, - FileFormat.Pfam); - AlignmentI al = new AppletFormatAdapter().readFile( - "ASEQ/15-25" + '\t' + "...--FFAFAFF--", - AppletFormatAdapter.PASTE, "PFAM"); ++ AlignmentI al = new AppletFormatAdapter().readFile("ASEQ/15-25" + '\t' ++ + "...--FFAFAFF--", DataSourceType.PASTE, FileFormat.Pfam); Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences"); Assert.assertTrue(al.hasValidSequence(), "Didn't extract limits from PFAM ID"); diff --cc test/jalview/structure/Mapping.java index 13387db,9ec3a92..ceb098b --- a/test/jalview/structure/Mapping.java +++ b/test/jalview/structure/Mapping.java @@@ -69,7 -68,7 +69,7 @@@ public class Mappin StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager(); StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot }, new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb", - jalview.io.DataSourceType.FILE); - jalview.io.FormatAdapter.FILE); ++ DataSourceType.FILE); assertTrue(pmap != null); SequenceI protseq = pmap.getSeqsAsArray()[0]; AlignmentAnnotation pstra = protseq @@@ -139,8 -138,8 +139,8 @@@ // Associate the 1GAQ pdb file with the subsequence 'imported' from another // source StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq }, - new String[] { "A" }, inFile = "examples/1gaq.txt", - jalview.io.FormatAdapter.FILE); + new String[] - { "A" }, inFile = "examples/1gaq.txt", jalview.io.DataSourceType.FILE); ++ { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE); assertTrue("PDB File couldn't be found", pde != null); StructureMapping[] mp = ssm.getMapping(inFile); assertTrue("No mappings made.", mp != null && mp.length > 0); @@@ -237,7 -236,7 +237,7 @@@ StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager(); StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq }, new String[] { null }, "examples/3W5V.pdb", - jalview.io.DataSourceType.FILE); - jalview.io.FormatAdapter.FILE); ++ DataSourceType.FILE); if (pmap == null) { AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE"); @@@ -254,7 -253,7 +254,7 @@@ StructureImportSettings.setShowSeqFeatures(true); AlignFrame ref = new FileLoader(false) .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb", - jalview.io.DataSourceType.FILE); - jalview.io.FormatAdapter.FILE); ++ DataSourceType.FILE); SequenceI refseq = ref.getViewport().getAlignment().getSequenceAt(0); SequenceI newseq = new Sequence(refseq.getName() + "Copy", refseq.getSequenceAsString()); @@@ -266,7 -265,7 +266,7 @@@ ssm.setAddTempFacAnnot(true); StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq }, new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb", - jalview.io.DataSourceType.FILE); - jalview.io.FormatAdapter.FILE); ++ DataSourceType.FILE); assertTrue(pmap != null); assertEquals("Original and copied sequence of different lengths.", refseq.getLength(), newseq.getLength()); diff --cc test/jalview/structures/models/AAStructureBindingModelTest.java index 2e0692e,66e0152..1dcbd44 --- a/test/jalview/structures/models/AAStructureBindingModelTest.java +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@@ -97,14 -110,14 +110,14 @@@ public class AAStructureBindingModelTes seqs[2] = new SequenceI[] { seq3 }; StructureSelectionManager ssm = new StructureSelectionManager(); - ssm.setMapping(new SequenceI[] { seq1 }, null, PDB_1, + ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1, - AppletFormatAdapter.PASTE); + DataSourceType.PASTE); ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2, - AppletFormatAdapter.PASTE); + DataSourceType.PASTE); ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3, - AppletFormatAdapter.PASTE); + DataSourceType.PASTE); - testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null) + testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null) { @Override public String[] getPdbFile() diff --cc test/jalview/ws/sifts/SiftsClientTest.java index 9d59b78,3f67c4c..9f6e306 --- a/test/jalview/ws/sifts/SiftsClientTest.java +++ b/test/jalview/ws/sifts/SiftsClientTest.java @@@ -471,4 -472,34 +472,34 @@@ public class SiftsClientTes Assert.assertEquals(entityD.getEntityId(), "D"); } + + @Test(groups = { "Functional" }) + public void getEntityByMostOptimalMatchedIdTest2() + { + // This test is for a SIFTS file in which entity A should map to chain P for + // the given PDB Id. All the other chains shouldn't be mapped as there are + // no SIFTS entity records for them. + SiftsClient siftsClientX = null; + PDBfile pdbFile; + try + { + pdbFile = new PDBfile(false, false, false, - "test/jalview/io/3ucu.cif", AppletFormatAdapter.FILE); ++ "test/jalview/io/3ucu.cif", DataSourceType.FILE); + siftsClientX = new SiftsClient(pdbFile); + } catch (Exception e) + { + e.printStackTrace(); + } + Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("P"); + Entity entityP = siftsClientX.getEntityByMostOptimalMatchedId("A"); + Entity entityR = siftsClientX.getEntityByMostOptimalMatchedId("R"); + Assert.assertEquals(entityA.getEntityId(), "A"); + Assert.assertNotEquals(entityR, "A"); + Assert.assertNotEquals(entityP, "A"); + Assert.assertNotEquals(entityR, "R"); + Assert.assertNotEquals(entityP, "P"); + Assert.assertNull(entityR); + Assert.assertNull(entityP); + + } }