From: Jim Procter Date: Mon, 4 Jul 2016 10:38:02 +0000 (+0100) Subject: Merge branch 'develop' into spike/JAL-2040_JAL-2137_phyre2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1e2d0cb3851160eb3e7ba9ec39a04a28a82e57e9;hp=e84b575bede2d5a6dea85cb96000dc751d090016;p=jalview.git Merge branch 'develop' into spike/JAL-2040_JAL-2137_phyre2 --- diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 3b84ee3..248cf29 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -82,7 +82,7 @@ public class PDBChain public PDBChain(String pdbid, String id) { - this.pdbid = pdbid.toLowerCase(); + this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase(); this.id = id; } @@ -357,18 +357,6 @@ public class PDBChain else { - // boolean baseDetected = false; - // for (Atom resAtom : resAtoms) - // { - // if (resAtom.insCode == ' ') - // { - // baseDetected = true; - // } - // } - // if (!baseDetected) - // { - // continue; - // } // Make a new Residue object with the new atoms vector residues.addElement(new Residue(resAtoms, resNumber - 1, count)); @@ -378,7 +366,6 @@ public class PDBChain SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset + count, offset + count, pdbid); - // MCview.PDBChain.PDBFILEFEATURE); resFeatures.addElement(sf); resAnnotation.addElement(new Annotation(tmpat.tfactor)); // Keep totting up the sequence diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 38aa55f..dde67de 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -21,7 +21,7 @@ package jalview.bin; import jalview.datamodel.DBRefSource; -import jalview.ws.dbsources.Pdb; +import jalview.structure.StructureViewSettings; import jalview.ws.dbsources.das.api.DasSourceRegistryI; import jalview.ws.dbsources.das.datamodel.DasSourceRegistry; import jalview.ws.sifts.SiftsSettings; @@ -426,7 +426,8 @@ public class Cache System.out .println("Jalview Version: " + codeVersion + codeInstallation); - Pdb.setCurrentDefaultFormat(jalview.bin.Cache.getDefault( + StructureViewSettings.setCurrentDefaultFormat(jalview.bin.Cache + .getDefault( "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT)); // jnlpVersion will be null if we're using InstallAnywhere // Dont do this check if running in headless mode diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index 0cbd620..309e196 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -206,6 +206,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener List significantAtoms = new ArrayList(); for (org.jmol.modelset.Atom atom : ms.at) { + // System.out.println("Seq Id : " + atom.getSeqID()); + // System.out.println("To String : " + atom.toString()); + if (atom.isHetero()) + { + continue; + } if (atom.getAtomName().equalsIgnoreCase("CA") || atom.getAtomName().equalsIgnoreCase("P")) { diff --git a/src/jalview/fts/api/GFTSPanelI.java b/src/jalview/fts/api/GFTSPanelI.java index ce63576..f86c3bc 100644 --- a/src/jalview/fts/api/GFTSPanelI.java +++ b/src/jalview/fts/api/GFTSPanelI.java @@ -21,6 +21,8 @@ package jalview.fts.api; +import java.util.Map; + import javax.swing.JTable; /** @@ -127,4 +129,12 @@ public interface GFTSPanelI * @param isEnabled */ public void setNextPageButtonEnabled(boolean isEnabled); + + /** + * The HashMap used to store user preferences for summary table columns, + * window size and position + * + * @return + */ + public Map getTempUserPrefs(); } diff --git a/src/jalview/fts/core/FTSRestResponse.java b/src/jalview/fts/core/FTSRestResponse.java index 8078d43..92ea5f8 100644 --- a/src/jalview/fts/core/FTSRestResponse.java +++ b/src/jalview/fts/core/FTSRestResponse.java @@ -25,6 +25,7 @@ import jalview.fts.api.FTSData; import jalview.fts.api.FTSDataColumnI; import java.util.Collection; +import java.util.Map; import javax.swing.JTable; import javax.swing.table.DefaultTableModel; @@ -134,7 +135,8 @@ public class FTSRestResponse } public static void configureTableColumn(JTable tbl_summary, - Collection wantedFields) + Collection wantedFields, + Map columnPrefs) { for (FTSDataColumnI wantedField : wantedFields) { @@ -144,8 +146,11 @@ public class FTSRestResponse wantedField.getMinWidth()); tbl_summary.getColumn(wantedField.getName()).setMaxWidth( wantedField.getMaxWidth()); + int prefedWidth = columnPrefs.get(wantedField.getName()) == null ? wantedField + .getPreferredWidth() : columnPrefs.get(wantedField + .getName()); tbl_summary.getColumn(wantedField.getName()).setPreferredWidth( - wantedField.getPreferredWidth()); + prefedWidth); } catch (Exception e) { e.printStackTrace(); @@ -153,15 +158,15 @@ public class FTSRestResponse if (wantedField.getDataType().getDataTypeClass() == Double.class) { DecimalFormatTableCellRenderer dfr = new DecimalFormatTableCellRenderer( - wantedField.getDataType().isFormtted(), - wantedField.getDataType().getSignificantFigures()); + wantedField.getDataType().isFormtted(), wantedField + .getDataType().getSignificantFigures()); tbl_summary.getColumn(wantedField.getName()).setCellRenderer(dfr); } else if (wantedField.getDataType().getDataTypeClass() == Integer.class) { DecimalFormatTableCellRenderer dfr = new DecimalFormatTableCellRenderer( - wantedField.getDataType().isFormtted(), - wantedField.getDataType().getSignificantFigures()); + wantedField.getDataType().isFormtted(), wantedField + .getDataType().getSignificantFigures()); tbl_summary.getColumn(wantedField.getName()).setCellRenderer(dfr); } } diff --git a/src/jalview/fts/core/GFTSPanel.java b/src/jalview/fts/core/GFTSPanel.java index b288aa5..33fa020 100644 --- a/src/jalview/fts/core/GFTSPanel.java +++ b/src/jalview/fts/core/GFTSPanel.java @@ -66,6 +66,7 @@ import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; +import javax.swing.event.InternalFrameEvent; import javax.swing.table.DefaultTableModel; import javax.swing.table.TableColumn; @@ -146,7 +147,6 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI protected static final DecimalFormat totalNumberformatter = new DecimalFormat( "###,###"); - private JTable tbl_summary = new JTable() { private boolean inLayout; @@ -190,6 +190,8 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI && !inLayout) { resizingColumn.setPreferredWidth(resizingColumn.getWidth()); + String colHeader = resizingColumn.getHeaderValue().toString(); + getTempUserPrefs().put(colHeader, resizingColumn.getWidth()); } resizeAndRepaint(); } @@ -244,6 +246,10 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI */ private void jbInit() throws Exception { + Integer width = getTempUserPrefs().get("FTSPanel.width") == null ? 800 + : getTempUserPrefs().get("FTSPanel.width"); + Integer height = getTempUserPrefs().get("FTSPanel.height") == null ? 400 + : getTempUserPrefs().get("FTSPanel.height"); lbl_warning.setVisible(false); lbl_warning.setFont(new java.awt.Font("Verdana", 0, 12)); lbl_loading.setVisible(false); @@ -428,7 +434,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI } } }); - scrl_searchResult.setPreferredSize(new Dimension(800, 400)); + scrl_searchResult.setPreferredSize(new Dimension(width, height)); cmb_searchTarget.setFont(new java.awt.Font("Verdana", 0, 12)); cmb_searchTarget.addActionListener(new ActionListener() @@ -571,7 +577,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI } }; tabbedPane.addChangeListener(changeListener); - tabbedPane.setPreferredSize(new Dimension(800, 400)); + tabbedPane.setPreferredSize(new Dimension(width, height)); tabbedPane.add(searchTabTitle, scrl_searchResult); tabbedPane.add(configureCols, new FTSDataColumnPreferences( PreferenceSource.SEARCH_SUMMARY, getFTSRestClient())); @@ -596,9 +602,40 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI mainFrame.setVisible(true); mainFrame.setContentPane(this); mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); - Desktop.addInternalFrame(mainFrame, getFTSFrameTitle(), 900, 500); + mainFrame + .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosing(InternalFrameEvent e) + { + closeAction(); + } + }); + mainFrame.setVisible(true); + mainFrame.setContentPane(this); + mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); + Integer x = getTempUserPrefs().get("FTSPanel.x"); + Integer y = getTempUserPrefs().get("FTSPanel.y"); + if (x != null && y != null) + { + mainFrame.setLocation(x, y); + } + Desktop.addInternalFrame(mainFrame, getFTSFrameTitle(), width, height); } + protected void closeAction() + { + // System.out.println(">>>>>>>>>> closing internal frame!!!"); + // System.out.println("width : " + this.getWidth()); + // System.out.println("heigh : " + this.getHeight()); + // System.out.println("x : " + mainFrame.getX()); + // System.out.println("y : " + mainFrame.getY()); + getTempUserPrefs().put("FTSPanel.width", this.getWidth()); + getTempUserPrefs().put("FTSPanel.height", pnl_results.getHeight()); + getTempUserPrefs().put("FTSPanel.x", mainFrame.getX()); + getTempUserPrefs().put("FTSPanel.y", mainFrame.getY()); + mainFrame.dispose(); + } public class DeferredTextInputListener implements DocumentListener { private final Timer swingTimer; @@ -719,7 +756,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI protected void btn_back_ActionPerformed() { - mainFrame.dispose(); + closeAction(); new SequenceFetcher(progressIdicator); } @@ -732,7 +769,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI protected void btn_cancel_ActionPerformed() { - mainFrame.dispose(); + closeAction(); } /** diff --git a/src/jalview/fts/service/pdb/PDBFTSPanel.java b/src/jalview/fts/service/pdb/PDBFTSPanel.java index 32c171e..5f5c716 100644 --- a/src/jalview/fts/service/pdb/PDBFTSPanel.java +++ b/src/jalview/fts/service/pdb/PDBFTSPanel.java @@ -29,7 +29,9 @@ import jalview.fts.core.GFTSPanel; import jalview.gui.SequenceFetcher; import jalview.util.MessageManager; +import java.util.HashMap; import java.util.HashSet; +import java.util.Map; @SuppressWarnings("serial") public class PDBFTSPanel extends GFTSPanel @@ -39,6 +41,8 @@ public class PDBFTSPanel extends GFTSPanel private String ftsFrameTitle = defaultFTSFrameTitle; + private static Map tempUserPrefs = new HashMap(); + public PDBFTSPanel(SequenceFetcher seqFetcher) { pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize(); @@ -101,7 +105,7 @@ public class PDBFTSPanel extends GFTSPanel FTSRestResponse.getTableModel(request, resultList.getSearchSummary())); FTSRestResponse.configureTableColumn(getResultTable(), - wantedFields); + wantedFields, tempUserPrefs); getResultTable().setVisible(true); } @@ -267,4 +271,10 @@ public class PDBFTSPanel extends GFTSPanel return true; } + @Override + public Map getTempUserPrefs() + { + return tempUserPrefs; + } + } diff --git a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java index b1aa5f1..9c2c5ce 100644 --- a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java +++ b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java @@ -29,7 +29,9 @@ import jalview.fts.core.GFTSPanel; import jalview.gui.SequenceFetcher; import jalview.util.MessageManager; +import java.util.HashMap; import java.util.HashSet; +import java.util.Map; @SuppressWarnings("serial") public class UniprotFTSPanel extends GFTSPanel @@ -40,7 +42,7 @@ public class UniprotFTSPanel extends GFTSPanel private String ftsFrameTitle = defaultFTSFrameTitle; - + private static Map tempUserPrefs = new HashMap(); public UniprotFTSPanel(SequenceFetcher seqFetcher) { @@ -104,7 +106,7 @@ public class UniprotFTSPanel extends GFTSPanel FTSRestResponse.getTableModel(request, resultList.getSearchSummary())); FTSRestResponse.configureTableColumn(getResultTable(), - wantedFields); + wantedFields, tempUserPrefs); getResultTable().setVisible(true); } @@ -225,4 +227,10 @@ public class UniprotFTSPanel extends GFTSPanel return ftsFrameTitle; } + @Override + public Map getTempUserPrefs() + { + return tempUserPrefs; + } + } diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 8bccc6b..13fa460 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -457,7 +457,7 @@ public class StructureChooser extends GStructureChooser implements lastPdbRequest, reorderedStructuresSet)); FTSRestResponse.configureTableColumn(getResultTable(), - wantedFields); + wantedFields, tempUserPrefs); getResultTable().getColumn("Ref Sequence").setPreferredWidth(120); getResultTable().getColumn("Ref Sequence").setMinWidth(100); getResultTable().getColumn("Ref Sequence").setMaxWidth(200); @@ -834,7 +834,7 @@ public class StructureChooser extends GStructureChooser implements launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new SequenceI[] { selectedSequence }); } - mainFrame.dispose(); + closeAction(); } }).start(); } diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index 1a639f1..42a8ead 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -280,7 +280,8 @@ public class AppletFormatAdapter { // TODO obtain config value from preference settings. // Set value to 'true' to test PDB processing with Jmol: JAL-1213 - boolean isParseWithJMOL = false; + boolean isParseWithJMOL = !StructureViewSettings + .getCurrentDefaultFormat().equalsIgnoreCase("PDB"); if (isParseWithJMOL) { StructureViewSettings.addSettings(annotFromStructure, @@ -291,6 +292,8 @@ public class AppletFormatAdapter } else { + StructureViewSettings.addSettings(annotFromStructure, + localSecondaryStruct, serviceSecondaryStruct); StructureViewSettings.setShowSeqFeatures(true); alignFile = new MCview.PDBfile(annotFromStructure, localSecondaryStruct, serviceSecondaryStruct, inFile, diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java index 44f659d..e571064 100644 --- a/src/jalview/jbgui/GStructureChooser.java +++ b/src/jalview/jbgui/GStructureChooser.java @@ -44,6 +44,8 @@ import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.Arrays; +import java.util.HashMap; +import java.util.Map; import javax.swing.ImageIcon; import javax.swing.JButton; @@ -61,6 +63,7 @@ import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; +import javax.swing.event.InternalFrameEvent; import javax.swing.table.TableColumn; @SuppressWarnings("serial") @@ -171,6 +174,8 @@ public abstract class GStructureChooser extends JPanel implements protected FTSDataColumnI[] previousWantedFields; + protected static Map tempUserPrefs = new HashMap(); + private JTable tbl_summary = new JTable() { private boolean inLayout; @@ -214,6 +219,8 @@ public abstract class GStructureChooser extends JPanel implements && !inLayout) { resizingColumn.setPreferredWidth(resizingColumn.getWidth()); + String colHeader = resizingColumn.getHeaderValue().toString(); + tempUserPrefs.put(colHeader, resizingColumn.getWidth()); } resizeAndRepaint(); } @@ -269,6 +276,10 @@ public abstract class GStructureChooser extends JPanel implements */ private void jbInit() throws Exception { + Integer width = tempUserPrefs.get("structureChooser.width") == null ? 800 + : tempUserPrefs.get("structureChooser.width"); + Integer height = tempUserPrefs.get("structureChooser.height") == null ? 400 + : tempUserPrefs.get("structureChooser.height"); tbl_summary.setAutoCreateRowSorter(true); tbl_summary.getTableHeader().setReorderingAllowed(false); tbl_summary.addMouseListener(new MouseAdapter() @@ -402,7 +413,7 @@ public abstract class GStructureChooser extends JPanel implements @Override public void actionPerformed(ActionEvent e) { - mainFrame.dispose(); + closeAction(); } }); btn_cancel.addKeyListener(new KeyAdapter() @@ -412,7 +423,7 @@ public abstract class GStructureChooser extends JPanel implements { if (evt.getKeyCode() == KeyEvent.VK_ENTER) { - mainFrame.dispose(); + closeAction(); } } }); @@ -440,9 +451,9 @@ public abstract class GStructureChooser extends JPanel implements } }); - scrl_foundStructures.setPreferredSize(new Dimension(800, 400)); + scrl_foundStructures.setPreferredSize(new Dimension(width, height)); - scrl_localPDB.setPreferredSize(new Dimension(800, 400)); + scrl_localPDB.setPreferredSize(new Dimension(width, height)); scrl_localPDB .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); @@ -538,7 +549,7 @@ public abstract class GStructureChooser extends JPanel implements } }; pnl_filter.addChangeListener(changeListener); - pnl_filter.setPreferredSize(new Dimension(800, 400)); + pnl_filter.setPreferredSize(new Dimension(width, height)); pnl_filter.add(foundStructureSummary, scrl_foundStructures); pnl_filter.add(configureCols, pdbDocFieldPrefs); @@ -559,12 +570,40 @@ public abstract class GStructureChooser extends JPanel implements statusPanel.add(statusBar, null); this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH); + mainFrame + .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosing(InternalFrameEvent e) + { + closeAction(); + } + }); mainFrame.setVisible(true); mainFrame.setContentPane(this); mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); - Desktop.addInternalFrame(mainFrame, frameTitle, 900, 500); + Integer x = tempUserPrefs.get("structureChooser.x"); + Integer y = tempUserPrefs.get("structureChooser.y"); + if (x != null && y != null) + { + mainFrame.setLocation(x, y); + } + Desktop.addInternalFrame(mainFrame, frameTitle, width, height); } + protected void closeAction() + { + // System.out.println(">>>>>>>>>> closing internal frame!!!"); + // System.out.println("width : " + mainFrame.getWidth()); + // System.out.println("heigh : " + mainFrame.getHeight()); + // System.out.println("x : " + mainFrame.getX()); + // System.out.println("y : " + mainFrame.getY()); + tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth()); + tempUserPrefs.put("structureChooser.height", pnl_filter.getHeight()); + tempUserPrefs.put("structureChooser.x", mainFrame.getX()); + tempUserPrefs.put("structureChooser.y", mainFrame.getY()); + mainFrame.dispose(); + } public boolean wantedFieldsUpdated() { if (previousWantedFields == null) diff --git a/src/jalview/structure/StructureViewSettings.java b/src/jalview/structure/StructureViewSettings.java index 2fcb3e5..5880d0f 100644 --- a/src/jalview/structure/StructureViewSettings.java +++ b/src/jalview/structure/StructureViewSettings.java @@ -1,5 +1,7 @@ package jalview.structure; +import jalview.datamodel.DBRefSource; + public class StructureViewSettings { private String dbRefType; @@ -24,6 +26,8 @@ public class StructureViewSettings private static boolean showSeqFeatures = true; + private static String currentDefaultFormat = DBRefSource.PDB; + public static void addSettings(boolean addAlignmentAnnotations, boolean predictSecStr, boolean externalSecStr) { @@ -76,4 +80,14 @@ public class StructureViewSettings StructureViewSettings.showSeqFeatures = showSeqFeatures; } + public static String getCurrentDefaultFormat() + { + return currentDefaultFormat; + } + + public static void setCurrentDefaultFormat(String currentDefaultFormat) + { + StructureViewSettings.currentDefaultFormat = currentDefaultFormat; + } + } diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java index b0b5e92..d3a6238 100644 --- a/src/jalview/ws/dbsources/Pdb.java +++ b/src/jalview/ws/dbsources/Pdb.java @@ -30,6 +30,7 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.io.FormatAdapter; import jalview.io.PDBFeatureSettings; +import jalview.structure.StructureViewSettings; import jalview.util.MessageManager; import jalview.ws.ebi.EBIFetchClient; @@ -54,8 +55,6 @@ public class Pdb extends EbiFileRetrievedProxy public static final String FEATURE_RES_NUM = "RESNUM"; - private static String currentDefaultFormat = DBRefSource.PDB; - /* * (non-Javadoc) * @@ -133,11 +132,13 @@ public class Pdb extends EbiFileRetrievedProxy stopQuery(); return null; } - String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif" + String ext = StructureViewSettings.getCurrentDefaultFormat() + .equalsIgnoreCase("mmcif") ? ".cif" : ".xml"; EBIFetchClient ebi = new EBIFetchClient(); file = ebi.fetchDataAsFile("pdb:" + id, - getCurrentDefaultFormat().toLowerCase(), ext) + StructureViewSettings.getCurrentDefaultFormat().toLowerCase(), + ext) .getAbsolutePath(); stopQuery(); if (file == null) @@ -149,7 +150,7 @@ public class Pdb extends EbiFileRetrievedProxy pdbAlignment = new FormatAdapter().readFile(file, jalview.io.AppletFormatAdapter.FILE, - getCurrentDefaultFormat()); + StructureViewSettings.getCurrentDefaultFormat()); if (pdbAlignment != null) { List toremove = new ArrayList(); @@ -264,15 +265,6 @@ public class Pdb extends EbiFileRetrievedProxy return 0; } - public static String getCurrentDefaultFormat() - { - return currentDefaultFormat; - } - - public static void setCurrentDefaultFormat(String currentDefaultFomart) - { - Pdb.currentDefaultFormat = currentDefaultFomart; - } /** * Returns a descriptor for suitable feature display settings with diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java index b560f01..27d2643 100644 --- a/test/jalview/ws/PDBSequenceFetcherTest.java +++ b/test/jalview/ws/PDBSequenceFetcherTest.java @@ -25,6 +25,7 @@ import static org.testng.AssertJUnit.assertTrue; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; +import jalview.structure.StructureViewSettings; import jalview.ws.seqfetcher.DbSourceProxy; import java.util.List; @@ -60,6 +61,10 @@ public class PDBSequenceFetcherTest @Test(groups = { "Network" }, enabled = true) public void testRnaSeqRetrieve() throws Exception { + Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("DEFAULT_STRUCTURE_FORMAT", + "PDB"); List sps = sf.getSourceProxy("PDB"); AlignmentI response = sps.get(0).getSequenceRecords("2GIS"); assertTrue(response != null); @@ -81,6 +86,8 @@ public class PDBSequenceFetcherTest { Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", Boolean.TRUE.toString()); + StructureViewSettings.setCurrentDefaultFormat("PDB"); + testRetrieveProteinSeqFromPDB(); } @@ -88,7 +95,8 @@ public class PDBSequenceFetcherTest public void testmmCifSeqRetrieve() throws Exception { Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", - Boolean.FALSE.toString()); + Boolean.TRUE.toString()); + StructureViewSettings.setCurrentDefaultFormat("mmCIF"); testRetrieveProteinSeqFromPDB(); }