import jalview.bin.Cache;
import jalview.gui.Preferences;
+import jalview.util.FileUtils;
+ import jalview.util.Platform;
import java.io.File;
import java.io.IOException;
pathList.add("/usr/local/chimera/bin/chimera");
pathList.add("/usr/local/bin/chimera");
pathList.add("/usr/bin/chimera");
- pathList.add(System.getProperty("user.home") + "/opt/bin/chimera");
+ pathList.add(Platform.getUserPath("opt/bin/chimera"));
}
else if (os.startsWith("Windows"))
{
- for (String root : new String[] { "\\Program Files",
- "C:\\Program Files", "\\Program Files (x86)",
- "C:\\Program Files (x86)" })
- {
- for (String version : new String[] { "1.11", "1.11.1", "1.11.2",
- "1.12", "1.12.1", "1.12.2", "1.13" })
- {
- pathList.add(root + "\\Chimera " + version + "\\bin\\chimera");
- pathList.add(
- root + "\\Chimera " + version + "\\bin\\chimera.exe");
- }
- }
+ /*
+ * typical Windows installation path is
+ * C:\Program Files\Chimera 1.12\bin\chimera.exe
+ */
+ // current drive:
+ pathList.addAll(FileUtils.findMatches("\\",
+ "Program Files*/Chimera*/bin/{chimera,chimera.exe}"));
+ // C: drive (note may add as duplicates)
+ pathList.addAll(FileUtils.findMatches("C:\\",
+ "Program Files*/Chimera*/bin/{chimera,chimera.exe}"));
}
else if (os.startsWith("Mac"))
{
import jalview.analysis.scoremodels.PIDModel;
import jalview.analysis.scoremodels.SimilarityParams;
+ import jalview.bin.ApplicationSingletonProvider;
+ import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.util.QuickSort;
import java.util.ArrayList;
+ import java.util.BitSet;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
* from the first tobesorted position in the alignment. e.g. (a,tb2,b,tb1,c,tb3
* becomes a,tb1,tb2,tb3,b,c)
*/
- public class AlignmentSorter
+ public class AlignmentSorter implements ApplicationSingletonI
{
+
+ private AlignmentSorter()
+ {
+ // private singleton
+ }
+
+ public static AlignmentSorter getInstance()
+ {
+ return (AlignmentSorter) ApplicationSingletonProvider
+ .getInstance(AlignmentSorter.class);
+ }
+
+ /**
+ * types of feature ordering: Sort by score : average score - or total score -
+ * over all features in region Sort by feature label text: (or if null -
+ * feature type text) - numerical or alphabetical Sort by feature density:
+ * based on counts - ignoring individual text or scores for each feature
+ */
+ public static final String FEATURE_SCORE = "average_score";
+
+ public static final String FEATURE_LABEL = "text";
+
+ public static final String FEATURE_DENSITY = "density";
+
/*
* todo: refactor searches to follow a basic pattern: (search property, last
* search state, current sort direction)
*/
- static boolean sortIdAscending = true;
+ boolean sortIdAscending = true;
- static int lastGroupHash = 0;
+ int lastGroupHash = 0;
- static boolean sortGroupAscending = true;
+ boolean sortGroupAscending = true;
- static AlignmentOrder lastOrder = null;
+ AlignmentOrder lastOrder = null;
- static boolean sortOrderAscending = true;
+ boolean sortOrderAscending = true;
- static TreeModel lastTree = null;
+ TreeModel lastTree = null;
- static boolean sortTreeAscending = true;
+ boolean sortTreeAscending = true;
- /*
+ /**
* last Annotation Label used for sort by Annotation score
*/
- private static String lastSortByAnnotation;
+ private String lastSortByAnnotation;
- /*
- * string hash of last arguments to sortByFeature
- * (sort order toggles if this is unchanged between sorts)
+ /**
+ * string hash of last arguments to sortByFeature (sort order toggles if this
+ * is unchanged between sorts)
*/
- private static String sortByFeatureCriteria;
+ private String sortByFeatureCriteria;
- private static boolean sortByFeatureAscending = true;
+ private boolean sortByFeatureAscending = true;
- private static boolean sortLengthAscending;
+ private boolean sortLengthAscending;
+ private static boolean sortEValueAscending;
+
+ private static boolean sortBitScoreAscending;
+
/**
* Sorts sequences in the alignment by Percentage Identity with the given
* reference sequence, sorting the highest identity to the top
}
QuickSort.sort(scores, seqs);
-
setReverseOrder(align, seqs);
}
/**
- * Reverse the order of the sort
- *
- * @param align
- * DOCUMENT ME!
- * @param seqs
- * DOCUMENT ME!
- */
- private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
- {
- int nSeq = seqs.length;
-
- int len = 0;
-
- if ((nSeq % 2) == 0)
- {
- len = nSeq / 2;
- }
- else
- {
- len = (nSeq + 1) / 2;
- }
-
- // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- List<SequenceI> asq = align.getSequences();
- synchronized (asq)
- {
- for (int i = 0; i < len; i++)
- {
- // SequenceI tmp = seqs[i];
- asq.set(i, seqs[nSeq - i - 1]);
- asq.set(nSeq - i - 1, seqs[i]);
- }
- }
- }
-
- /**
- * Sets the Alignment object with the given sequences
- *
- * @param align
- * Alignment object to be updated
- * @param tmp
- * sequences as a vector
- */
- private static void setOrder(AlignmentI align, List<SequenceI> tmp)
- {
- setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
- }
-
- /**
- * Sets the Alignment object with the given sequences
- *
- * @param align
- * DOCUMENT ME!
- * @param seqs
- * sequences as an array
- */
- public static void setOrder(AlignmentI align, SequenceI[] seqs)
- {
- // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- List<SequenceI> algn = align.getSequences();
- synchronized (algn)
- {
- List<SequenceI> tmp = new ArrayList<>();
-
- for (int i = 0; i < seqs.length; i++)
- {
- if (algn.contains(seqs[i]))
- {
- tmp.add(seqs[i]);
- }
- }
-
- algn.clear();
- // User may have hidden seqs, then clicked undo or redo
- for (int i = 0; i < tmp.size(); i++)
- {
- algn.add(tmp.get(i));
- }
- }
- }
-
- /**
* Sorts by ID. Numbers are sorted before letters.
*
* @param align
}
QuickSort.sort(ids, seqs);
-
- if (sortIdAscending)
- {
- setReverseOrder(align, seqs);
- }
- else
- {
- setOrder(align, seqs);
- }
-
- sortIdAscending = !sortIdAscending;
+ AlignmentSorter as = getInstance();
+ as.sortIdAscending = !as.sortIdAscending;
+ set(align, seqs, as.sortIdAscending);
}
/**
}
QuickSort.sort(length, seqs);
-
- if (sortLengthAscending)
- {
- setReverseOrder(align, seqs);
- }
- else
- {
- setOrder(align, seqs);
- }
-
- sortLengthAscending = !sortLengthAscending;
+ AlignmentSorter as = getInstance();
+ as.sortLengthAscending = !as.sortLengthAscending;
+ set(align, seqs, as.sortLengthAscending);
}
/**
+ * Sorts by sequence evalue. Currently moves all sequences without an evalue to
+ * the top of the alignment.
+ *
+ * @param align
+ * The alignment object to sort
+ */
+ public static void sortByEValue(AlignmentI align)
+ {
+ int nSeq = align.getHeight();
+
+ double[] evalue = new double[nSeq];
+ SequenceI[] seqs = new SequenceI[nSeq];
+
+ for (int i = 0; i < nSeq; i++)
+ {
+ seqs[i] = align.getSequenceAt(i);
+ AlignmentAnnotation[] ann = seqs[i].getAnnotation("Search Scores");
+ if (ann != null)
+ {
+ evalue[i] = ann[0].getEValue();
+ }
+ else
+ {
+ evalue[i] = -1;
+ }
+ }
+
+ QuickSort.sort(evalue, seqs);
+
+ if (sortEValueAscending)
+ {
+ setReverseOrder(align, seqs);
+ }
+ else
+ {
+ setOrder(align, seqs);
+ }
+
+ sortEValueAscending = !sortEValueAscending;
+ }
+
+ /**
+ * Sorts by sequence bit score. Currently moves all sequences without a bit
+ * score to the top of the alignment
+ *
+ * @param align
+ * The alignment object to sort
+ */
+ public static void sortByBitScore(AlignmentI align)
+ {
+ int nSeq = align.getHeight();
+
+ double[] score = new double[nSeq];
+ SequenceI[] seqs = new SequenceI[nSeq];
+
+ for (int i = 0; i < nSeq; i++)
+ {
+ seqs[i] = align.getSequenceAt(i);
+ AlignmentAnnotation[] ann = seqs[i].getAnnotation("Search Scores");
+ if (ann != null)
+ {
+ score[i] = ann[0].getEValue();
+ }
+ else
+ {
+ score[i] = -1;
+ }
+ }
+
+ QuickSort.sort(score, seqs);
+
+ if (sortBitScoreAscending)
+ {
+ setReverseOrder(align, seqs);
+ }
+ else
+ {
+ setOrder(align, seqs);
+ }
+
+ sortBitScoreAscending = !sortBitScoreAscending;
+ }
+
+ /**
* Sorts the alignment by size of group. <br>
* Maintains the order of sequences in each group by order in given alignment
* object.
// ORDERS BY GROUP SIZE
List<SequenceGroup> groups = new ArrayList<>();
- if (groups.hashCode() != lastGroupHash)
+ AlignmentSorter as = getInstance();
+
+ if (groups.hashCode() != as.lastGroupHash)
{
- sortGroupAscending = true;
- lastGroupHash = groups.hashCode();
+ as.sortGroupAscending = true;
+ as.lastGroupHash = groups.hashCode();
}
else
{
- sortGroupAscending = !sortGroupAscending;
+ as.sortGroupAscending = !as.sortGroupAscending;
}
// SORTS GROUPS BY SIZE
// NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
// /////////////////////////////////////////////
- List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceI> tmp = new ArrayList<>();
for (int i = 0; i < groups.size(); i++)
{
for (int j = 0; j < orderedseqs.length; j++)
{
- seqs.add(orderedseqs[j]);
- }
- }
-
- if (sortGroupAscending)
- {
- setOrder(align, seqs);
- }
- else
- {
- setReverseOrder(align,
- vectorSubsetToArray(seqs, align.getSequences()));
- }
- }
-
- /**
- * Select sequences in order from tmp that is present in mask, and any
- * remaining sequences in mask not in tmp
- *
- * @param tmp
- * thread safe collection of sequences
- * @param mask
- * thread safe collection of sequences
- *
- * @return intersect(tmp,mask)+intersect(complement(tmp),mask)
- */
- private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
- List<SequenceI> mask)
- {
- // or?
- // tmp2 = tmp.retainAll(mask);
- // return tmp2.addAll(mask.removeAll(tmp2))
-
- ArrayList<SequenceI> seqs = new ArrayList<>();
- int i, idx;
- boolean[] tmask = new boolean[mask.size()];
-
- for (i = 0; i < mask.size(); i++)
- {
- tmask[i] = true;
- }
-
- for (i = 0; i < tmp.size(); i++)
- {
- SequenceI sq = tmp.get(i);
- idx = mask.indexOf(sq);
- if (idx > -1 && tmask[idx])
- {
- tmask[idx] = false;
- seqs.add(sq);
- }
- }
-
- for (i = 0; i < tmask.length; i++)
- {
- if (tmask[i])
- {
- seqs.add(mask.get(i));
+ tmp.add(orderedseqs[j]);
}
}
-
- return seqs.toArray(new SequenceI[seqs.size()]);
+ set(align, tmp, as.sortGroupAscending);
}
/**
// Get an ordered vector of sequences which may also be present in align
List<SequenceI> tmp = order.getOrder();
- if (lastOrder == order)
- {
- sortOrderAscending = !sortOrderAscending;
- }
- else
- {
- sortOrderAscending = true;
- }
+ AlignmentSorter as = getInstance();
- if (sortOrderAscending)
+ if (as.lastOrder == order)
{
- setOrder(align, tmp);
+ as.sortOrderAscending = !as.sortOrderAscending;
}
else
{
- setReverseOrder(align,
- vectorSubsetToArray(tmp, align.getSequences()));
+ as.sortOrderAscending = true;
}
+ set(align, tmp, as.sortOrderAscending);
}
/**
{
List<SequenceI> tmp = getOrderByTree(align, tree);
- // tmp should properly permute align with tree.
- if (lastTree != tree)
- {
- sortTreeAscending = true;
- lastTree = tree;
- }
- else
- {
- sortTreeAscending = !sortTreeAscending;
- }
+ AlignmentSorter as = getInstance();
- if (sortTreeAscending)
+ // tmp should properly permute align with tree.
+ if (as.lastTree != tree)
{
- setOrder(align, tmp);
+ as.sortTreeAscending = true;
+ as.lastTree = tree;
}
else
{
- setReverseOrder(align,
- vectorSubsetToArray(tmp, align.getSequences()));
+ as.sortTreeAscending = !as.sortTreeAscending;
}
+ set(align, tmp, as.sortTreeAscending);
}
/**
}
jalview.util.QuickSort.sort(scores, seqs);
- if (lastSortByAnnotation != scoreLabel)
+
+ AlignmentSorter as = getInstance();
+
+ if (as.lastSortByAnnotation != scoreLabel)
{
- lastSortByAnnotation = scoreLabel;
+ as.lastSortByAnnotation = scoreLabel;
setOrder(alignment, seqs);
}
else
}
/**
- * types of feature ordering: Sort by score : average score - or total score -
- * over all features in region Sort by feature label text: (or if null -
- * feature type text) - numerical or alphabetical Sort by feature density:
- * based on counts - ignoring individual text or scores for each feature
- */
- public static String FEATURE_SCORE = "average_score";
-
- public static String FEATURE_LABEL = "text";
-
- public static String FEATURE_DENSITY = "density";
-
- /**
* Sort sequences by feature score or density, optionally restricted by
* feature types, feature groups, or alignment start/end positions.
* <p>
if (method != FEATURE_SCORE && method != FEATURE_LABEL
&& method != FEATURE_DENSITY)
{
- String msg = String
- .format("Implementation Error - sortByFeature method must be either '%s' or '%s'",
- FEATURE_SCORE, FEATURE_DENSITY);
+ String msg = String.format(
+ "Implementation Error - sortByFeature method must be either '%s' or '%s'",
+ FEATURE_SCORE, FEATURE_DENSITY);
System.err.println(msg);
return;
}
- flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol, endCol);
+ flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol,
+ endCol);
SequenceI[] seqs = alignment.getSequencesArray();
* get sequence residues overlapping column region
* and features for residue positions and specified types
*/
- String[] types = featureTypes == null ? null : featureTypes
- .toArray(new String[featureTypes.size()]);
+ String[] types = featureTypes == null ? null
+ : featureTypes.toArray(new String[featureTypes.size()]);
List<SequenceFeature> sfs = seqs[i].findFeatures(startCol + 1,
endCol + 1, types);
}
}
+ boolean doSort = false;
+
if (FEATURE_SCORE.equals(method))
{
if (hasScores == 0)
}
}
}
- QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);
+ doSort = true;
}
else if (FEATURE_DENSITY.equals(method))
{
// System.err.println("Sorting on Density: seq "+seqs[i].getName()+
// " Feats: "+featureCount+" Score : "+scores[i]);
}
- QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);
+ doSort = true;
+ }
+ if (doSort)
+ {
+ QuickSort.sortByDouble(scores, seqs,
+ getInstance().sortByFeatureAscending);
}
-
setOrder(alignment, seqs);
}
/*
* if resorting on the same criteria, toggle sort order
*/
- if (sortByFeatureCriteria == null
- || !scoreCriteria.equals(sortByFeatureCriteria))
+ AlignmentSorter as = getInstance();
+ if (as.sortByFeatureCriteria == null
+ || !scoreCriteria.equals(as.sortByFeatureCriteria))
{
- sortByFeatureAscending = true;
+ as.sortByFeatureAscending = true;
}
else
{
- sortByFeatureAscending = !sortByFeatureAscending;
+ as.sortByFeatureAscending = !as.sortByFeatureAscending;
}
- sortByFeatureCriteria = scoreCriteria;
+ as.sortByFeatureCriteria = scoreCriteria;
+ }
+
+ /**
+ * Set the alignment's sequences list to contain the sequences from a
+ * temporary list, first adding all the elements from the tmp list, then adding all sequences in the alignment that
+ * are not in the list. Option to do the final sort either in order or in reverse order.
+ *
+ * @param align The alignment being sorted
+ * @param tmp
+ * the temporary sequence list
+ * @param ascending
+ * false for reversed order; only sequences already in
+ * the alignment will be used (which is actually already guaranteed
+ * by vectorSubsetToArray)
+ */
+ private static void set(AlignmentI align, List<SequenceI> tmp,
+ boolean ascending)
+ {
+ set(align, vectorSubsetToArray(align.getSequences(), tmp), ascending);
+ }
+
+ /**
+ * Set the alignment's sequences list to contain these sequences, either in
+ * this order or its reverse.
+ *
+ * @param align
+ * @param seqs
+ * the new sequence array
+ * @param ascending
+ * false for reversed order; if ascending, only sequences already in
+ * the alignment will be used; if descending, then a direct 1:1
+ * replacement is made
+ */
+ private static void set(AlignmentI align, SequenceI[] seqs,
+ boolean ascending)
+ {
+ if (ascending)
+ {
+ setOrder(align, seqs);
+ }
+ else
+ {
+ setReverseOrder(align, seqs);
+ }
+
+ }
+
+ /**
+ * Replace the alignment's sequences with values in an array, clearing the
+ * alignment's sequence list and filtering for sequences that are actually in
+ * the alignment already.
+ *
+ * @param align
+ * the Alignment
+ * @param seqs
+ * the array of replacement values, of any length
+ */
+ public static void setOrder(AlignmentI align, SequenceI[] seqs)
+ {
+ // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+ List<SequenceI> seqList = align.getSequences();
+ synchronized (seqList)
+ {
+ List<SequenceI> tmp = new ArrayList<>();
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqList.contains(seqs[i]))
+ {
+ tmp.add(seqs[i]);
+ }
+ }
+
+ seqList.clear();
+ // User may have hidden seqs, then clicked undo or redo
+ for (int i = 0; i < tmp.size(); i++)
+ {
+ seqList.add(tmp.get(i));
+ }
+ }
+ }
+
+ /**
+ * Replace the alignment's sequences or a subset of those sequences with
+ * values in an array in reverse order. All sequences are replaced; no check
+ * is made that these sequences are in the alignment already.
+ *
+ * @param align
+ * the Alignment
+ * @param seqs
+ * the array of replacement values, length must be less than or equal
+ * to Alignment.sequences.size()
+ */
+ private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
+ {
+ int nSeq = seqs.length;
+
+ int len = (nSeq + (nSeq % 2)) / 2;
+ // int len = 0;
+ //
+ // if ((nSeq % 2) == 0)
+ // {
+ // len = nSeq / 2;
+ // }
+ // else
+ // {
+ // len = (nSeq + 1) / 2;
+ // }
+
+ // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+ List<SequenceI> seqList = align.getSequences();
+ synchronized (seqList)
+ {
+ for (int i = 0; i < len; i++)
+ {
+ // SequenceI tmp = seqs[i];
+ seqList.set(i, seqs[nSeq - i - 1]);
+ seqList.set(nSeq - i - 1, seqs[i]);
+ }
+ }
+ }
+
+ /**
+ * Create and array of reordered sequences in order first from tmp that are
+ * present in seqList already, then, after that, any remaining sequences in
+ * seqList not in tmp. Any sequences in tmp that are not in seqList already
+ * are discarded.
+ *
+ * @param seqList
+ * thread safe collection of sequences originally in the alignment
+ * @param tmp
+ * thread safe collection of sequences or subsequences possibly in
+ * seqList
+ *
+ * @return intersect(tmp,seqList)+intersect(complement(tmp),seqList)
+ */
+ private static SequenceI[] vectorSubsetToArray(List<SequenceI> seqList,
+ List<SequenceI> tmp)
+ {
+ ArrayList<SequenceI> seqs = new ArrayList<>();
+ int n = seqList.size();
+ BitSet bs = new BitSet(n);
+ bs.set(0, n);
+ for (int i = 0, nt = tmp.size(); i < nt; i++)
+ {
+ SequenceI sq = tmp.get(i);
+ int idx = seqList.indexOf(sq);
+ if (idx >= 0 && bs.get(idx))
+ {
+ seqs.add(sq);
+ bs.clear(idx);
+ }
+ }
+
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ {
+ seqs.add(seqList.get(i));
+ }
+
+ return seqs.toArray(new SequenceI[seqs.size()]);
}
}
alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
+ viewport.initInformationWorker(alignPanel);
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
followMouseOverFlag.setState(viewport.isFollowHighlight());
}
else if (source == autoCalculate)
{
- viewport.autoCalculateConsensus = autoCalculate.getState();
+ viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
}
else if (source == sortByTree)
{
{
sortGroupMenuItem_actionPerformed();
}
+ else if (source == sortEValueMenuItem)
+ {
+ sortEValueMenuItem_actionPerformed();
+ }
+ else if (source == sortBitScoreMenuItem)
+ {
+ sortBitScoreMenuItem_actionPerformed();
+ }
else if (source == removeRedundancyMenuItem)
{
removeRedundancyMenuItem_actionPerformed();
// viewport.getColumnSelection().getHiddenColumns()
// != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- originalSource.getAlignment().getSequences());
+ originalSource.notifyAlignment();
}
/**
// != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- originalSource.getAlignment().getSequences());
+ originalSource.notifyAlignment();
}
AlignmentViewport getOriginatingSource(CommandI command)
viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
// 2019.04.18
viewport.getAlignment().getWidth();
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
}
viewport.setSelectionGroup(null);
viewport.getAlignment().deleteGroup(sg);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
if (viewport.getAlignment().getHeight() < 1)
{
}
}
- viewport.firePropertyChange("alignment", null, al.getSequences());
+ viewport.notifyAlignment();
}
}
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
ranges.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, al.getSequences());
+ viewport.notifyAlignment();
}
ranges.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, al.getSequences());
+ viewport.notifyAlignment();
}
}
+ public void sortEValueMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByEValue(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+
+ public void sortBitScoreMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByBitScore(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+
public void removeRedundancyMenuItem_actionPerformed()
{
new RedundancyPanel(alignPanel);
MenuItem sortGroupMenuItem = new MenuItem();
+ MenuItem sortEValueMenuItem = new MenuItem();
+
+ MenuItem sortBitScoreMenuItem = new MenuItem();
+
MenuItem removeRedundancyMenuItem = new MenuItem();
MenuItem pairwiseAlignmentMenuItem = new MenuItem();
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
*
* This file is part of Jalview.
*
private AnnotationColumnChooser annotationColumnSelectionState;
+ java.awt.Frame nullFrame;
+
+ protected FeatureSettings featureSettings = null;
+
+ private float heightScale = 1, widthScale = 1;
+
public AlignViewport(AlignmentI al, JalviewLite applet)
{
super(al);
- calculator = new jalview.workers.AlignCalcManager();
+ calculator = new jalview.workers.AlignCalcManager2();
this.applet = applet;
// we always pad gaps
colour));
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(consensusProfiles);
}
}
}
}
initAutoAnnotation();
-
}
- java.awt.Frame nullFrame;
-
- protected FeatureSettings featureSettings = null;
-
- private float heightScale = 1, widthScale = 1;
-
/**
* {@inheritDoc}
*/
.getStructureSelectionManager(applet);
}
- @Override
- public boolean isNormaliseSequenceLogo()
- {
- return normaliseSequenceLogo;
- }
-
- public void setNormaliseSequenceLogo(boolean state)
- {
- normaliseSequenceLogo = state;
- }
-
/**
*
* @return true if alignment characters should be displayed
if (mappedCommand != null)
{
mappedCommand.doCommand(null);
- firePropertyChange("alignment", null, getAlignment().getSequences());
+ notifyAlignment();
// ap.scalePanelHolder.repaint();
// ap.repaint();
*/
package jalview.appletgui;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
++import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.event.MouseMotionListener;
import java.beans.PropertyChangeEvent;
+ import jalview.datamodel.AlignmentAnnotation;
+ import jalview.datamodel.Annotation;
+ import jalview.datamodel.SequenceI;
+ import jalview.renderer.AnnotationRenderer;
+ import jalview.renderer.AwtRenderPanelI;
+ import jalview.schemes.ResidueProperties;
+ import jalview.util.Comparison;
+ import jalview.util.MessageManager;
+ import jalview.viewmodel.ViewportListenerI;
+ import jalview.viewmodel.ViewportRanges;
+
public class AnnotationPanel extends Panel
implements AwtRenderPanelI, AdjustmentListener, ActionListener,
MouseListener, MouseMotionListener, ViewportListenerI
import java.awt.Graphics;
import java.awt.Insets;
import java.awt.Panel;
-
++import java.awt.event.WindowAdapter;
++import java.awt.event.WindowEvent;
public class TitledPanel extends Panel
{
*/
package jalview.bin;
- import jalview.ext.so.SequenceOntology;
- import jalview.gui.AlignFrame;
- import jalview.gui.Desktop;
- import jalview.gui.PromptUserConfig;
- import jalview.io.AppletFormatAdapter;
- import jalview.io.BioJsHTMLOutput;
- import jalview.io.DataSourceType;
- import jalview.io.FileFormat;
- import jalview.io.FileFormatException;
- import jalview.io.FileFormatI;
- import jalview.io.FileLoader;
- import jalview.io.HtmlSvgOutput;
- import jalview.io.IdentifyFile;
- import jalview.io.NewickFile;
- import jalview.io.gff.SequenceOntologyFactory;
- import jalview.schemes.ColourSchemeI;
- import jalview.schemes.ColourSchemeProperty;
- import jalview.util.MessageManager;
- import jalview.util.Platform;
- import jalview.ws.jws2.Jws2Discoverer;
-
+ import java.awt.GraphicsEnvironment;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.util.HashMap;
import java.util.Map;
import java.util.Vector;
- import java.util.logging.ConsoleHandler;
- import java.util.logging.Level;
- import java.util.logging.Logger;
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
+ import jalview.api.AlignCalcWorkerI;
+ import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+ import jalview.ext.so.SequenceOntology;
+ import jalview.gui.AlignFrame;
+ import jalview.gui.AlignViewport;
+ import jalview.gui.Desktop;
+ import jalview.gui.Preferences;
+ import jalview.gui.PromptUserConfig;
+ import jalview.io.AppletFormatAdapter;
+ import jalview.io.BioJsHTMLOutput;
+ import jalview.io.DataSourceType;
+ import jalview.io.FileFormat;
+ import jalview.io.FileFormatException;
+ import jalview.io.FileFormatI;
+ import jalview.io.FileFormats;
+ import jalview.io.FileLoader;
+ import jalview.io.HtmlSvgOutput;
+ import jalview.io.IdentifyFile;
+ import jalview.io.NewickFile;
+ import jalview.io.gff.SequenceOntologyFactory;
+ import jalview.schemes.ColourSchemeI;
+ import jalview.schemes.ColourSchemeProperty;
+ import jalview.util.MessageManager;
+ import jalview.util.Platform;
+ import jalview.ws.jws2.Jws2Discoverer;
/**
* Main class for Jalview Application <br>
* @author $author$
* @version $Revision$
*/
- public class Jalview
+ public class Jalview implements ApplicationSingletonI
{
- static
+
+ // for testing those nasty messages you cannot ever find.
+ // static
+ // {
+ // System.setOut(new PrintStream(new ByteArrayOutputStream())
+ // {
+ // @Override
+ // public void println(Object o)
+ // {
+ // if (o != null)
+ // {
+ // System.err.println(o);
+ // }
+ // }
+ //
+ // });
+ // }
+ public static Jalview getInstance()
{
- Platform.getURLCommandArguments();
+ return (Jalview) ApplicationSingletonProvider
+ .getInstance(Jalview.class);
}
- // singleton instance of this class
+ private Jalview()
+ {
+ }
- private static Jalview instance;
+ private boolean headless;
private Desktop desktop;
- public static AlignFrame currentAlignFrame;
+ public AlignFrame currentAlignFrame;
+
+ public String appletResourcePath;
+
+ public String j2sAppletID;
+
+ private boolean noCalculation, noMenuBar, noStatus;
+
+ private boolean noAnnotation;
+
+ public boolean getStartCalculations()
+ {
+ return !noCalculation;
+ }
+
+ public boolean getAllowMenuBar()
+ {
+ return !noMenuBar;
+ }
+
+ public boolean getShowStatus()
+ {
+ return !noStatus;
+ }
+
+ public boolean getShowAnnotation()
+ {
+ return !noAnnotation;
+ }
static
{
- if (!Platform.isJS())
- /**
- * Java only
- *
- * @j2sIgnore
- */
+ if (Platform.isJS()) {
+ Platform.getURLCommandArguments();
+ } else /** @j2sIgnore */
{
// grab all the rights we can for the JVM
Policy.setPolicy(new Policy()
perms.add(new AllPermission());
return (perms);
}
-
+
@Override
public void refresh()
{
class FeatureFetcher
{
/*
- * TODO: generalise to track all jalview events to orchestrate batch processing
- * events.
+ * TODO: generalise to track all jalview events to orchestrate batch
+ * processing events.
*/
private int queued = 0;
}
- public static Jalview getInstance()
- {
- return instance;
- }
+ private final static boolean doPlatformLogging = false;
/**
* main class for Jalview application
*
* @param args
- * open <em>filename</em>
+ * open <em>filename</em>
*/
public static void main(String[] args)
{
- // setLogging(); // BH - for event debugging in JavaScript
- instance = new Jalview();
- instance.doMain(args);
- }
-
- private static void logClass(String name)
- {
- // BH - for event debugging in JavaScript
- ConsoleHandler consoleHandler = new ConsoleHandler();
- consoleHandler.setLevel(Level.ALL);
- Logger logger = Logger.getLogger(name);
- logger.setLevel(Level.ALL);
- logger.addHandler(consoleHandler);
- }
-
- @SuppressWarnings("unused")
- private static void setLogging()
- {
-
- /**
- * @j2sIgnore
- *
- */
+ if (doPlatformLogging)
{
- System.out.println("not in js");
+ Platform.startJavaLogging();
}
-
- // BH - for event debugging in JavaScript (Java mode only)
- if (!Platform.isJS())
- /**
- * Java only
- *
- * @j2sIgnore
- */
- {
- Logger.getLogger("").setLevel(Level.ALL);
- logClass("java.awt.EventDispatchThread");
- logClass("java.awt.EventQueue");
- logClass("java.awt.Component");
- logClass("java.awt.focus.Component");
- logClass("java.awt.focus.DefaultKeyboardFocusManager");
- }
-
+ getInstance().doMain(args);
}
-
-
-
/**
* @param args
void doMain(String[] args)
{
- if (!Platform.isJS())
+ boolean isJS = Platform.isJS();
+ if (!isJS)
{
System.setSecurityManager(null);
}
System.out
- .println("Java version: "
- + System.getProperty("java.version"));
+ .println("Java version: " + System.getProperty("java.version"));
System.out.println("Java Home: " + System.getProperty("java.home"));
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
String val = System.getProperty("sys.install4jVersion");
- if (val != null) {
- System.out.println("Install4j version: " + val);
+ if (val != null)
+ {
+ System.out.println("Install4j version: " + val);
}
val = System.getProperty("installer_template_version");
- if (val != null) {
+ if (val != null)
+ {
System.out.println("Install4j template version: " + val);
}
val = System.getProperty("launcher_version");
- if (val != null) {
+ if (val != null)
+ {
System.out.println("Launcher version: " + val);
}
// report Jalview version
- Cache.loadBuildProperties(true);
+ Cache.getInstance().loadBuildProperties(true);
ArgsParser aparser = new ArgsParser(args);
- boolean headless = false;
+ headless = false;
String usrPropsFile = aparser.getValue("props");
+
Cache.loadProperties(usrPropsFile); // must do this before
- if (usrPropsFile != null)
+
+ boolean allowServices = true;
+
+ if (isJS)
{
- System.out.println(
- "CMD [-props " + usrPropsFile + "] executed successfully!");
+ j2sAppletID = Platform.getAppID(null);
+ Preferences.setAppletDefaults();
+ Cache.loadProperties(usrPropsFile); // again, because we
+ // might be changing defaults here?
+ appletResourcePath = (String) aparser.getAppletValue("resourcepath",
+ null, true);
}
-
- if (!Platform.isJS())
+ else
/**
* Java only
*
* @j2sIgnore
*/
{
+
+ if (usrPropsFile != null)
+ {
+ System.out.println(
+ "CMD [-props " + usrPropsFile + "] executed successfully!");
+ }
if (aparser.contains("help") || aparser.contains("h"))
{
showUsage();
System.exit(0);
}
+ // BH note: Only -nodisplay is official; others are deprecated?
if (aparser.contains("nodisplay") || aparser.contains("nogui")
- || aparser.contains("headless"))
+ || aparser.contains("headless")
+ || GraphicsEnvironment.isHeadless())
{
- System.setProperty("java.awt.headless", "true");
+ if (!isJS) {
+ // BH Definitely not a good idea in JavaScript;
+ // probably should not be here for Java, either.
+ System.setProperty("java.awt.headless", "true");
+ }
headless = true;
}
- // anything else!
- final String jabawsUrl = aparser.getValue("jabaws");
- if (jabawsUrl != null)
+ final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
+ allowServices = !("none".equals(jabawsUrl));
+ if (allowServices && jabawsUrl != null)
{
try
{
- Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl);
System.out.println(
"CMD [-jabaws " + jabawsUrl + "] executed successfully!");
} catch (MalformedURLException e)
}
}
- String defs = aparser.getValue("setprop");
+ String defs = aparser.getValue(ArgsParser.SETPROP);
while (defs != null)
{
int p = defs.indexOf('=');
else
{
System.out.println("Executing setprop argument: " + defs);
- if (Platform.isJS())
+ if (isJS)
{
- Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+ Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
}
}
defs = aparser.getValue("setprop");
}
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
- {
- headless = true;
- }
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
try
System.exit(0);
}
- desktop = null;
-
- try
- {
- UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
- } catch (Exception ex)
+ if (!isJS)
+ /** @j2sIgnore */
{
- System.err.println("Unexpected Look and Feel Exception");
- ex.printStackTrace();
- }
- if (Platform.isAMacAndNotJS())
- {
-
- LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
- .getLookAndFeel();
- System.setProperty("com.apple.mrj.application.apple.menu.about.name",
- "Jalview");
- System.setProperty("apple.laf.useScreenMenuBar", "true");
- if (lookAndFeel != null)
+ try
{
- try
- {
- UIManager.setLookAndFeel(lookAndFeel);
- } catch (Throwable e)
- {
- System.err.println(
- "Failed to set QuaQua look and feel: " + e.toString());
- }
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+ } catch (Exception ex)
+ {
+ System.err.println("Unexpected Look and Feel Exception");
+ ex.printStackTrace();
}
- if (lookAndFeel == null
- || !(lookAndFeel.getClass().isAssignableFrom(
- UIManager.getLookAndFeel().getClass()))
- || !UIManager.getLookAndFeel().getClass().toString()
- .toLowerCase().contains("quaqua"))
+ if (Platform.isMac())
{
- try
+
+ LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
+ .getLookAndFeel();
+ System.setProperty(
+ "com.apple.mrj.application.apple.menu.about.name",
+ "Jalview");
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ if (lookAndFeel != null)
{
- System.err.println(
- "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
- UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
- } catch (Throwable e)
+ try
+ {
+ UIManager.setLookAndFeel(lookAndFeel);
+ } catch (Throwable e)
+ {
+ System.err.println(
+ "Failed to set QuaQua look and feel: " + e.toString());
+ }
+ }
+ if (lookAndFeel == null
+ || !(lookAndFeel.getClass().isAssignableFrom(
+ UIManager.getLookAndFeel().getClass()))
+ || !UIManager.getLookAndFeel().getClass().toString()
+ .toLowerCase().contains("quaqua"))
{
- System.err.println(
- "Failed to reset look and feel: " + e.toString());
+ try
+ {
+ System.err.println(
+ "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
+ UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
+ } catch (Throwable e)
+ {
+ System.err.println(
+ "Failed to reset look and feel: " + e.toString());
+ }
}
}
}
-
/*
* configure 'full' SO model if preferences say to, else use the default (full SO)
* - as JS currently doesn't have OBO parsing, it must use 'Lite' version
*/
- boolean soDefault = !Platform.isJS();
+ boolean soDefault = !isJS;
if (Cache.getDefault("USE_FULL_SO", soDefault))
{
- SequenceOntologyFactory.setInstance(new SequenceOntology());
+ SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
}
+
+ desktop = null;
if (!headless)
{
- desktop = new Desktop();
+ desktop = Desktop.getInstance();
desktop.setInBatchMode(true); // indicate we are starting up
-
try
{
JalviewTaskbar.setTaskbar(this);
{
System.out.println("Error setting Taskbar: " + t.getMessage());
}
-
desktop.setVisible(true);
-
+ if (Platform.isJS())
+ Cache.setProperty("SHOW_JWS2_SERVICES", "false");
- desktop.startServiceDiscovery();
-
- if (!Platform.isJS())
++ if (allowServices)
++ {
++ desktop.startServiceDiscovery();
++ }
+ if (!isJS)
/**
* Java only
*
* @j2sIgnore
*/
{
- if (allowServices)
- desktop.startServiceDiscovery();
if (!aparser.contains("nousagestats"))
{
startUsageStats(desktop);
BioJsHTMLOutput.updateBioJS();
}
}
+ parseArguments(aparser, true);
+ }
- // Move any new getdown-launcher-new.jar into place over old
- // getdown-launcher.jar
- String appdirString = System.getProperty("getdownappdir");
- if (appdirString != null && appdirString.length() > 0)
+ /**
+ * Parse all command-line String[] arguments as well as all JavaScript-derived
+ * parameters from Info.
+ *
+ * We allow for this method to be run from JavaScript. Basically allowing
+ * simple scripting.
+ *
+ * @param aparser
+ * @param isStartup
+ */
+ public void parseArguments(ArgsParser aparser, boolean isStartup)
+ {
+
+ String groovyscript = null; // script to execute after all loading is
+ boolean isJS = Platform.isJS();
+ if (!isJS)
+ /** @j2sIgnore */
{
- final File appdir = new File(appdirString);
- new Thread()
+ // Move any new getdown-launcher-new.jar into place over old
+ // getdown-launcher.jar
+ String appdirString = System.getProperty("getdownappdir");
+ if (appdirString != null && appdirString.length() > 0)
{
- @Override
- public void run()
+ final File appdir = new File(appdirString);
+ new Thread()
{
- LaunchUtil.upgradeGetdown(
- new File(appdir, "getdown-launcher-old.jar"),
- new File(appdir, "getdown-launcher.jar"),
- new File(appdir, "getdown-launcher-new.jar"));
- }
- }.start();
- }
+ @Override
+ public void run()
+ {
+ LaunchUtil.upgradeGetdown(
+ new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+ }.start();
+ }
- String file = null, data = null;
- FileFormatI format = null;
- DataSourceType protocol = null;
- FileLoader fileLoader = new FileLoader(!headless);
+ // completed one way or another
+ // extract groovy argument and execute if necessary
+ groovyscript = aparser.getValue("groovy", true);
- String groovyscript = null; // script to execute after all loading is
- // completed one way or another
- // extract groovy argument and execute if necessary
- groovyscript = aparser.getValue("groovy", true);
- file = aparser.getValue("open", true);
+ }
+
+ String file = aparser.getValue("open", true);
- if (file == null && desktop == null)
+ if (!isJS && file == null && desktop == null)
{
System.out.println("No files to open!");
System.exit(1);
}
+
+ setDisplayParameters(aparser);
+
+ // time to open a file.
+
long progress = -1;
+ DataSourceType protocol = null;
+ FileLoader fileLoader = new FileLoader(!headless);
+ FileFormatI format = null;
// Finally, deal with the remaining input data.
- if (file != null)
+ AlignFrame af = null;
+
+ JalviewJSApp jsApp = (isJS ? new JalviewJSApp(this, aparser) : null);
+
+ if (file == null)
+ {
+ if (isJS)
+ {
+ // JalviewJS allows sequence1 sequence2 ....
+
+ }
+ else if (!headless && Cache.getDefault("SHOW_STARTUP_FILE", true))
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+
+ // We'll only open the default file if the desktop is visible.
+ // And the user
+ // ////////////////////
+
+ file = Cache.getDefault("STARTUP_FILE",
+ Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org")
+ + "/examples/exampleFile_2_7.jar");
+ if (file.equals(
+ "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ {
+ // hardwire upgrade of the startup file
+ file.replace("_2_3.jar", "_2_7.jar");
+ // and remove the stale setting
+ Cache.removeProperty("STARTUP_FILE");
+ }
+
+ protocol = DataSourceType.FILE;
+
+ if (file.indexOf("http:") > -1)
+ {
+ protocol = DataSourceType.URL;
+ }
+
+ if (file.endsWith(".jar"))
+ {
+ format = FileFormat.Jalview;
+ }
+ else
+ {
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e)
+ {
+ // TODO what?
+ }
+ }
+ af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
+ }
+ }
+ else
{
if (!headless)
{
System.out.println("CMD [-open " + file + "] executed successfully!");
if (!Platform.isJS())
- /**
- * ignore in JavaScript -- can't just file existence - could load it?
- *
- * @j2sIgnore
- */
+ /**
+ * ignore in JavaScript -- can't just file existence - could load it?
+ *
+ * @j2sIgnore
+ */
{
if (!file.startsWith("http://") && !file.startsWith("https://"))
// BH 2019 added https check for Java
}
}
}
-
- protocol = AppletFormatAdapter.checkProtocol(file);
-
+
+ String fileFormat = (isJS
+ ? (String) aparser.getAppletValue("format", null, true)
+ : null);
+ protocol = AppletFormatAdapter.checkProtocol(file);
try
{
- format = new IdentifyFile().identify(file, protocol);
+ format = (fileFormat != null
+ ? FileFormats.getInstance().forName(fileFormat)
+ : null);
+ if (format == null)
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ }
} catch (FileFormatException e1)
{
// TODO ?
}
- AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+ af = new FileLoader(!headless).LoadFileWaitTillLoaded(file, protocol,
format);
if (af == null)
{
- System.out.println("error");
+ System.out.println("jalview error - AlignFrame was not created");
}
else
{
- setCurrentAlignFrame(af);
- data = aparser.getValue("colour", true);
- if (data != null)
- {
- data.replaceAll("%20", " ");
-
- ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
- af.getViewport(), af.getViewport().getAlignment(), data);
-
- if (cs != null)
- {
- System.out.println(
- "CMD [-color " + data + "] executed successfully!");
- }
- af.changeColour(cs);
- }
- // Must maintain ability to use the groups flag
- data = aparser.getValue("groups", true);
- if (data != null)
- {
- af.parseFeaturesFile(data,
- AppletFormatAdapter.checkProtocol(data));
- // System.out.println("Added " + data);
- System.out.println(
- "CMD groups[-" + data + "] executed successfully!");
- }
- data = aparser.getValue("features", true);
- if (data != null)
- {
- af.parseFeaturesFile(data,
- AppletFormatAdapter.checkProtocol(data));
- // System.out.println("Added " + data);
- System.out.println(
- "CMD [-features " + data + "] executed successfully!");
- }
-
- data = aparser.getValue("annotations", true);
- if (data != null)
- {
- af.loadJalviewDataFile(data, null, null, null);
- // System.out.println("Added " + data);
- System.out.println(
- "CMD [-annotations " + data + "] executed successfully!");
- }
- // set or clear the sortbytree flag.
- if (aparser.contains("sortbytree"))
+ // JalviewLite interface for JavaScript allows second file open
+ String file2 = aparser.getValue(ArgsParser.OPEN2, true);
+ if (file2 != null)
{
- af.getViewport().setSortByTree(true);
- if (af.getViewport().getSortByTree())
+ protocol = AppletFormatAdapter.checkProtocol(file2);
+ try
{
- System.out.println("CMD [-sortbytree] executed successfully!");
- }
- }
- if (aparser.contains("no-annotation"))
- {
- af.getViewport().setShowAnnotation(false);
- if (!af.getViewport().isShowAnnotation())
+ format = new IdentifyFile().identify(file2, protocol);
+ } catch (FileFormatException e1)
{
- System.out.println("CMD no-annotation executed successfully!");
+ // TODO ?
}
- }
- if (aparser.contains("nosortbytree"))
- {
- af.getViewport().setSortByTree(false);
- if (!af.getViewport().getSortByTree())
+ AlignFrame af2 = new FileLoader(!headless)
+ .LoadFileWaitTillLoaded(file2, protocol, format);
+ if (af2 == null)
{
- System.out
- .println("CMD [-nosortbytree] executed successfully!");
+ System.out.println("error");
}
- }
- data = aparser.getValue("tree", true);
- if (data != null)
- {
- try
+ else
{
+ AlignViewport.openLinkedAlignmentAs(af,
+ af.getViewport().getAlignment(),
+ af2.getViewport().getAlignment(), "",
+ AlignViewport.SPLIT_FRAME);
System.out.println(
- "CMD [-tree " + data + "] executed successfully!");
- NewickFile nf = new NewickFile(data,
- AppletFormatAdapter.checkProtocol(data));
- af.getViewport()
- .setCurrentTree(af.showNewickTree(nf, data).getTree());
- } catch (IOException ex)
- {
- System.err.println("Couldn't add tree " + data);
- ex.printStackTrace(System.err);
+ "CMD [-open2 " + file2 + "] executed successfully!");
}
}
- // TODO - load PDB structure(s) to alignment JAL-629
- // (associate with identical sequence in alignment, or a specified
- // sequence)
- if (groovyscript != null)
+ setCurrentAlignFrame(af);
+
+ setFrameDependentProperties(aparser, af);
+
+ if (isJS)
{
- // Execute the groovy script after we've done all the rendering stuff
- // and before any images or figures are generated.
- System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, af);
- System.out.println("CMD groovy[" + groovyscript
- + "] executed successfully!");
- groovyscript = null;
+ jsApp.initFromParams(af);
}
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- String outputFormat = aparser.nextValue();
- file = aparser.nextValue();
-
- if (outputFormat.equalsIgnoreCase("png"))
- {
- af.createPNG(new File(file));
- imageName = (new File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("svg"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- af.createSVG(imageFile);
- System.out.println("Creating SVG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("html"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(file);
-
- System.out.println("Creating HTML image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+ if (groovyscript != null)
{
- 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 (outputFormat.equalsIgnoreCase("imgMap"))
- {
- af.createImageMap(new File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("eps"))
- {
- File outputFile = new File(file);
- System.out.println(
- "Creating EPS file: " + outputFile.getAbsolutePath());
- af.createEPS(outputFile);
- continue;
- }
-
- af.saveAlignment(file, format);
- if (af.isSaveAlignmentSuccessful())
- {
- System.out.println("Written alignment in " + format
- + " format to " + file);
- }
- else
- {
- System.out.println("Error writing file " + file + " in "
- + format + " format!!");
+ // Execute the groovy script after we've done all the rendering
+ // stuff
+ // and before any images or figures are generated.
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, af);
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
+ groovyscript = null;
}
-
}
-
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
+ if (!isJS || !isStartup) {
+ createOutputFiles(aparser, format);
}
}
+ if (headless)
+ {
+ af.getViewport().getCalcManager().shutdown();
+ }
}
- AlignFrame startUpAlframe = null;
- // We'll only open the default file if the desktop is visible.
- // And the user
- // ////////////////////
+ // extract groovy arguments before anything else.
+ // Once all other stuff is done, execute any groovy scripts (in order)
+ if (!isJS && groovyscript != null)
+ {
+ if (Cache.groovyJarsPresent())
+ {
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, af);
+ }
+ else
+ {
+ System.err.println(
+ "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ + groovyscript);
+ }
+ }
- if (!Platform.isJS() && !headless && file == null
- && Cache.getDefault("SHOW_STARTUP_FILE", true))
- /**
- * Java only
- *
- * @j2sIgnore
- */
+ // and finally, turn off batch mode indicator - if the desktop still exists
+ if (desktop != null)
{
- file = Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
- + "/examples/exampleFile_2_7.jar");
- if (file.equals(
- "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ if (progress != -1)
{
- // hardwire upgrade of the startup file
- file.replace("_2_3.jar", "_2_7.jar");
- // and remove the stale setting
- Cache.removeProperty("STARTUP_FILE");
+ desktop.setProgressBar(null, progress);
}
+ desktop.setInBatchMode(false);
+ }
+
+ if (jsApp != null) {
+ jsApp.callInitCallback();
+ }
+ }
+
+ /**
+ * Set general display parameters irrespective of file loading or headlessness.
+ *
+ * @param aparser
+ */
+ private void setDisplayParameters(ArgsParser aparser)
+ {
+ if (aparser.contains(ArgsParser.NOMENUBAR))
+ {
+ noMenuBar = true;
+ System.out.println("CMD [nomenu] executed successfully!");
+ }
+
+ if (aparser.contains(ArgsParser.NOSTATUS))
+ {
+ noStatus = true;
+ System.out.println("CMD [nostatus] executed successfully!");
+ }
+
+ if (aparser.contains(ArgsParser.NOANNOTATION)
+ || aparser.contains(ArgsParser.NOANNOTATION2))
+ {
+ noAnnotation = true;
+ System.out.println("CMD no-annotation executed successfully!");
+ }
+ if (aparser.contains(ArgsParser.NOCALCULATION))
+ {
+ noCalculation = true;
+ System.out.println("CMD [nocalculation] executed successfully!");
+ }
+ }
+
+
+ private void setFrameDependentProperties(ArgsParser aparser,
+ AlignFrame af)
+ {
+ String data = aparser.getValue(ArgsParser.COLOUR, true);
+ if (data != null)
+ {
+ data.replaceAll("%20", " ");
- protocol = DataSourceType.FILE;
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
- if (file.indexOf("http:") > -1)
+ if (cs != null)
{
- protocol = DataSourceType.URL;
+ System.out.println(
+ "CMD [-color " + data + "] executed successfully!");
}
+ af.changeColour(cs);
+ }
+
+ // Must maintain ability to use the groups flag
+ data = aparser.getValue(ArgsParser.GROUPS, true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD groups[-" + data + "] executed successfully!");
+ }
+ data = aparser.getValue(ArgsParser.FEATURES, true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD [-features " + data + "] executed successfully!");
+ }
+ data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
+ if (data != null)
+ {
+ af.loadJalviewDataFile(data, null, null, null);
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD [-annotations " + data + "] executed successfully!");
+ }
+
+ // JavaScript feature
- if (file.endsWith(".jar"))
+ if (aparser.contains(ArgsParser.SHOWOVERVIEW))
+ {
+ af.overviewMenuItem_actionPerformed(null);
+ System.out.println("CMD [showoverview] executed successfully!");
+ }
+
+ // set or clear the sortbytree flag.
+ if (aparser.contains(ArgsParser.SORTBYTREE))
+ {
+ af.getViewport().setSortByTree(true);
+ if (af.getViewport().getSortByTree())
{
- format = FileFormat.Jalview;
+ System.out.println("CMD [-sortbytree] executed successfully!");
}
- else
+ }
+
+ boolean doUpdateAnnotation = false;
+ /**
+ * we do this earlier in JalviewJS because of a complication with
+ * SHOWOVERVIEW
+ *
+ * For now, just fixing this in JalviewJS.
+ *
+ *
+ * @j2sIgnore
+ *
+ */
+ {
+ if (noAnnotation)
{
- try
- {
- format = new IdentifyFile().identify(file, protocol);
- } catch (FileFormatException e)
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
{
- // TODO what?
+ doUpdateAnnotation = true;
}
}
-
- startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
- format);
- // extract groovy arguments before anything else.
}
- // Once all other stuff is done, execute any groovy scripts (in order)
- if (groovyscript != null)
+ if (aparser.contains(ArgsParser.NOSORTBYTREE))
{
- if (Cache.groovyJarsPresent())
+ af.getViewport().setSortByTree(false);
+ if (!af.getViewport().getSortByTree())
{
- System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, startUpAlframe);
+ doUpdateAnnotation = true;
+ System.out
+ .println("CMD [-nosortbytree] executed successfully!");
}
- else
+ }
+ if (doUpdateAnnotation)
+ { // BH 2019.07.24
+ af.setMenusForViewport();
+ af.alignPanel.updateLayout();
+ }
+
+ data = aparser.getValue(ArgsParser.TREE, true);
+ if (data != null)
+ {
+ try
{
- System.err.println(
- "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
- + groovyscript);
+ NewickFile nf = new NewickFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ af.getViewport()
+ .setCurrentTree(af.showNewickTree(nf, data).getTree());
+ System.out.println(
+ "CMD [-tree " + data + "] executed successfully!");
+ } catch (IOException ex)
+ {
+ System.err.println("Couldn't add tree " + data);
+ ex.printStackTrace(System.err);
}
}
- // and finally, turn off batch mode indicator - if the desktop still exists
- if (desktop != null)
+ // TODO - load PDB structure(s) to alignment JAL-629
+ // (associate with identical sequence in alignment, or a specified
+ // sequence)
+
+ }
+
+ /**
+ * Writes an output file for each format (if any) specified in the
+ * command-line arguments. Supported formats are currently
+ * <ul>
+ * <li>png</li>
+ * <li>svg</li>
+ * <li>html</li>
+ * <li>biojsmsa</li>
+ * <li>imgMap</li>
+ * <li>eps</li>
+ * </ul>
+ * A format parameter should be followed by a parameter specifying the output
+ * file name. {@code imgMap} parameters should follow those for the
+ * corresponding alignment image output.
+ *
+ * @param aparser
+ * @param format
+ */
+ private void createOutputFiles(ArgsParser aparser, FileFormatI format)
+ {
+ AlignFrame af = currentAlignFrame;
+ while (aparser.getSize() >= 2)
{
- if (progress != -1)
+ String outputFormat = aparser.nextValue();
+ File imageFile;
+ String fname;
+ switch (outputFormat.toLowerCase())
{
- desktop.setProgressBar(null, progress);
+ case "png":
+ imageFile = new File(aparser.nextValue());
+ af.createPNG(imageFile);
+ System.out.println(
+ "Creating PNG image: " + imageFile.getAbsolutePath());
+ continue;
+ case "svg":
+ imageFile = new File(aparser.nextValue());
+ af.createSVG(imageFile);
+ System.out.println(
+ "Creating SVG image: " + imageFile.getAbsolutePath());
+ continue;
+ case "eps":
+ imageFile = new File(aparser.nextValue());
+ System.out.println(
+ "Creating EPS file: " + imageFile.getAbsolutePath());
+ af.createEPS(imageFile);
+ continue;
+ case "biojsmsa":
+ fname = new File(aparser.nextValue()).getAbsolutePath();
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(fname);
+ System.out.println("Creating BioJS MSA Viwer HTML file: " + fname);
+ continue;
+ case "html":
+ fname = new File(aparser.nextValue()).getAbsolutePath();
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(fname);
+ System.out.println("Creating HTML image: " + fname);
+ continue;
+ case "imgmap":
+ imageFile = new File(aparser.nextValue());
+ af.alignPanel.makePNGImageMap(imageFile, "unnamed.png");
+ System.out.println(
+ "Creating image map: " + imageFile.getAbsolutePath());
+ continue;
+ default:
+ // fall through - try to parse as an alignment data export format
+ FileFormatI outFormat = null;
+ try
+ {
+ outFormat = FileFormats.getInstance().forName(outputFormat);
+ } catch (Exception formatP)
+ {
+ }
+ if (outFormat == null)
+ {
+ System.out.println("Couldn't parse " + outputFormat
+ + " as a valid Jalview format string.");
+ continue;
+ }
+ if (!outFormat.isWritable())
+ {
+ System.out.println(
+ "This version of Jalview does not support alignment export as "
+ + outputFormat);
+ continue;
+ }
+ // record file as it was passed to Jalview so it is recognisable to the CLI
+ // caller
+ String file;
+ fname = new File(file = aparser.nextValue()).getAbsolutePath();
+ // JBPNote - yuck - really wish we did have a bean returned from this which gave
+ // success/fail like before !
+ af.saveAlignment(fname, outFormat);
+ if (!af.isSaveAlignmentSuccessful())
+ {
+ System.out.println("Written alignment in " + outputFormat
+ + " format to " + file);
+ continue;
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + outputFormat + " format!!");
+ }
}
- desktop.setInBatchMode(false);
+ }
+ // ??? Should report - 'ignoring' extra args here...
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Ignoring extra argument: " + aparser.nextValue());
}
}
/**
* start a User Config prompt asking if we can log usage statistics.
*/
- PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
+ PromptUserConfig prompter = new PromptUserConfig(Desktop.getDesktopPane(),
"USAGESTATS", "Jalview Usage Statistics",
"Do you want to help make Jalview better by enabling "
+ "the collection of usage statistics with Google Analytics ?"
* Locate the given string as a file and pass it to the groovy interpreter.
*
* @param groovyscript
- * the script to execute
+ * the script to execute
* @param jalviewContext
- * the Jalview Desktop object passed in to the groovy
- * binding as the 'Jalview' object.
+ * the Jalview Desktop object passed in to the groovy binding as the
+ * 'Jalview' object.
*/
private void executeGroovyScript(String groovyscript, AlignFrame af)
{
}
/**
- * Quit method delegates to Desktop.quit - unless running in headless mode when
- * it just ends the JVM
+ * Quit method delegates to Desktop.quit - unless running in headless mode
+ * when it just ends the JVM
*/
public void quit()
{
public static AlignFrame getCurrentAlignFrame()
{
- return Jalview.currentAlignFrame;
+ return Jalview.getInstance().currentAlignFrame;
}
public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
{
- Jalview.currentAlignFrame = currentAlignFrame;
+ Jalview.getInstance().currentAlignFrame = currentAlignFrame;
}
+
+
+ public void notifyWorker(AlignCalcWorkerI worker, String status)
+ {
+ // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
+ // + " " + status);
+ }
+
+
+ private static boolean isInteractive = true;
+
+ public static boolean isInteractive()
+ {
+ return isInteractive;
+ }
+
+ public static void setInteractive(boolean tf)
+ {
+ isInteractive = tf;
+ }
+
}
}
/**
+ * Inserts a sequence at a point in the alignment.
+ *
+ * @param i
+ * the index of the position the sequence is to be inserted in.
+ */
+ @Override
+ public void insertSequenceAt(int i, SequenceI snew)
+ {
+ synchronized (sequences)
+ {
+ if (sequences.size() > i)
+ {
+ sequences.add(i, snew);
+ return;
+
+ }
+ else
+ {
+ sequences.add(snew);
+ hiddenSequences.adjustHeightSequenceAdded();
+ }
+ return;
+ }
+ }
+
+ /**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
@Override
public SequenceI findName(SequenceI startAfter, String token, boolean b)
{
-
+ if (token == null)
+ return null;
int i = 0;
SequenceI sq = null;
String sqname = null;
String calcId, boolean autoCalc, SequenceI seqRef,
SequenceGroup groupRef)
{
- if (annotations != null)
+ AlignmentAnnotation annot = annotations == null ? null
+ : AlignmentAnnotation.findFirstAnnotation(
+ Arrays.asList(getAlignmentAnnotation()), name, calcId,
+ autoCalc, seqRef, groupRef);
+
+ if (annot == null)
{
- for (AlignmentAnnotation annot : getAlignmentAnnotation())
+
+ annot = new AlignmentAnnotation(name, name, new Annotation[1], 0f, 0f,
+ AlignmentAnnotation.BAR_GRAPH);
+ annot.hasText = false;
+ if (calcId != null)
{
- if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
- && (calcId == null || annot.getCalcId().equals(calcId))
- && annot.sequenceRef == seqRef
- && annot.groupRef == groupRef)
- {
- return annot;
- }
+ annot.setCalcId(calcId);
}
+ annot.autoCalculated = autoCalc;
+ if (seqRef != null)
+ {
+ annot.setSequenceRef(seqRef);
+ }
+ annot.groupRef = groupRef;
+ addAnnotation(annot);
}
- AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
- new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
- annot.hasText = false;
- if (calcId != null)
+ return annot;
+ }
+
+
+ @Override
+ public AlignmentAnnotation updateFromOrCopyAnnotation(
+ AlignmentAnnotation ala)
+ {
+ AlignmentAnnotation annot = AlignmentAnnotation.findFirstAnnotation(
+ Arrays.asList(getAlignmentAnnotation()), ala.label, ala.calcId,
+ ala.autoCalculated, ala.sequenceRef, ala.groupRef);
+ if (annot == null)
{
- annot.setCalcId(new String(calcId));
+ annot = new AlignmentAnnotation(ala);
+ addAnnotation(annot);
}
- annot.autoCalculated = autoCalc;
- if (seqRef != null)
+ else
{
- annot.setSequenceRef(seqRef);
+ annot.updateAlignmentAnnotationFrom(ala);
}
- annot.groupRef = groupRef;
- addAnnotation(annot);
-
+ validateAnnotation(annot);
return annot;
}
}
}
+ @Override
+ public List<SequenceI> getHmmSequences()
+ {
+ List<SequenceI> result = new ArrayList<>();
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ SequenceI seq = sequences.get(i);
+ if (seq.hasHMMProfile())
+ {
+ result.add(seq);
+ }
+ }
+ return result;
+ }
}
*/
package jalview.gui;
- import java.awt.BorderLayout;
- import java.awt.Color;
- import java.awt.Component;
- import java.awt.Rectangle;
- import java.awt.Toolkit;
- import java.awt.datatransfer.Clipboard;
- import java.awt.datatransfer.DataFlavor;
- import java.awt.datatransfer.StringSelection;
- import java.awt.datatransfer.Transferable;
- import java.awt.dnd.DnDConstants;
- import java.awt.dnd.DropTargetDragEvent;
- import java.awt.dnd.DropTargetDropEvent;
- import java.awt.dnd.DropTargetEvent;
- import java.awt.dnd.DropTargetListener;
- import java.awt.event.ActionEvent;
- import java.awt.event.ActionListener;
- import java.awt.event.FocusAdapter;
- import java.awt.event.FocusEvent;
- import java.awt.event.ItemEvent;
- import java.awt.event.ItemListener;
- import java.awt.event.KeyAdapter;
- import java.awt.event.KeyEvent;
- import java.awt.event.MouseEvent;
- import java.awt.print.PageFormat;
- import java.awt.print.PrinterJob;
- import java.beans.PropertyChangeListener;
- import java.io.File;
- import java.io.FileWriter;
- import java.io.PrintWriter;
- import java.net.URL;
- import java.util.ArrayList;
- import java.util.Arrays;
- import java.util.Collection;
- import java.util.Deque;
- import java.util.List;
- import java.util.Vector;
-
- import javax.swing.ButtonGroup;
- import javax.swing.JCheckBoxMenuItem;
- import javax.swing.JComponent;
- import javax.swing.JEditorPane;
- import javax.swing.JInternalFrame;
- import javax.swing.JLabel;
- import javax.swing.JLayeredPane;
- import javax.swing.JMenu;
- import javax.swing.JMenuItem;
- import javax.swing.JPanel;
- import javax.swing.JScrollPane;
- import javax.swing.SwingUtilities;
- import javax.swing.event.InternalFrameAdapter;
- import javax.swing.event.InternalFrameEvent;
-
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.CrossRef;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.hmmer.HMMAlign;
+import jalview.hmmer.HMMBuild;
+import jalview.hmmer.HMMERParamStore;
+import jalview.hmmer.HMMERPreset;
+import jalview.hmmer.HMMSearch;
+import jalview.hmmer.HmmerCommand;
+import jalview.hmmer.JackHMMER;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BackupFiles;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.ServiceChangeListener;
+import jalview.ws.WSDiscovererI;
+import jalview.ws.api.ServiceWithParameters;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.PreferredServiceRegistry;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.slivkaws.SlivkaWSDiscoverer;
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+ import java.awt.BorderLayout;
+ import java.awt.Color;
+ import java.awt.Component;
+ import java.awt.Dimension;
+ import java.awt.Rectangle;
+ import java.awt.Toolkit;
+ import java.awt.datatransfer.Clipboard;
+ import java.awt.datatransfer.DataFlavor;
+ import java.awt.datatransfer.StringSelection;
+ import java.awt.datatransfer.Transferable;
+ import java.awt.dnd.DnDConstants;
+ import java.awt.dnd.DropTargetDragEvent;
+ import java.awt.dnd.DropTargetDropEvent;
+ import java.awt.dnd.DropTargetEvent;
+ import java.awt.dnd.DropTargetListener;
+ import java.awt.event.ActionEvent;
+ import java.awt.event.ActionListener;
+ import java.awt.event.FocusAdapter;
+ import java.awt.event.FocusEvent;
+ import java.awt.event.ItemEvent;
+ import java.awt.event.ItemListener;
+ import java.awt.event.KeyAdapter;
+ import java.awt.event.KeyEvent;
+ import java.awt.event.MouseEvent;
+ import java.awt.print.PageFormat;
+ import java.awt.print.PrinterJob;
+ import java.beans.PropertyChangeEvent;
++import java.beans.PropertyChangeListener;
+ import java.io.File;
+ import java.io.FileWriter;
+ import java.io.PrintWriter;
+ import java.net.URL;
+ import java.util.ArrayList;
+ import java.util.Arrays;
++import java.util.Collection;
+ import java.util.Deque;
+ import java.util.Enumeration;
+ import java.util.Hashtable;
+ import java.util.List;
+ import java.util.Vector;
+
+ import javax.swing.ButtonGroup;
+ import javax.swing.JCheckBoxMenuItem;
+ import javax.swing.JComponent;
+ import javax.swing.JEditorPane;
+ import javax.swing.JInternalFrame;
+ import javax.swing.JLabel;
+ import javax.swing.JLayeredPane;
+ import javax.swing.JMenu;
+ import javax.swing.JMenuItem;
+ import javax.swing.JPanel;
+ import javax.swing.JScrollPane;
+ import javax.swing.SwingUtilities;
++import javax.swing.event.InternalFrameAdapter;
++import javax.swing.event.InternalFrameEvent;
+
+ import ext.vamsas.ServiceHandle;
+
/**
* DOCUMENT ME!
*
* @version $Revision$
*/
@SuppressWarnings("serial")
-public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
+public class AlignFrame extends GAlignFrame
+ implements DropTargetListener, IProgressIndicator,
+ AlignViewControllerGuiI, ColourChangeListener, ServiceChangeListener
{
+
+ public static int frameCount;
+
public static final int DEFAULT_WIDTH = 700;
public static final int DEFAULT_HEIGHT = 500;
*/
String fileName = null;
+ /**
+ * TODO: remove reference to 'FileObject' in AlignFrame - not correct mapping
+ */
File fileObject;
+ private int id;
+
+ private DataSourceType protocol ;
+
/**
* Creates a new AlignFrame object with specific width and height.
*
public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
int height, String sequenceSetId, String viewId)
{
+
+ id = (++frameCount);
+
setSize(width, height);
if (al.getDataset() == null)
viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
- alignPanel = new AlignmentPanel(this, viewport);
-
- addAlignmentPanel(alignPanel, true);
+ // JalviewJS needs to distinguish a new panel from an old one in init()
+ // alignPanel = new AlignmentPanel(this, viewport);
+ // addAlignmentPanel(alignPanel, true);
init();
}
{
viewport.hideSequence(hiddenSeqs);
}
- alignPanel = new AlignmentPanel(this, viewport);
- addAlignmentPanel(alignPanel, true);
+ // alignPanel = new AlignmentPanel(this, viewport);
+ // addAlignmentPanel(alignPanel, true);
init();
}
{
viewport = ap.av;
alignPanel = ap;
- addAlignmentPanel(ap, false);
+ // addAlignmentPanel(ap, false);
init();
}
* initalise the alignframe from the underlying viewport data and the
* configurations
*/
+
void init()
{
-
+ boolean newPanel = (alignPanel == null);
+ viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ if (newPanel)
+ {
+ if (Platform.isJS())
+ {
+ // need to set this up front if NOANNOTATION is
+ // used in conjunction with SHOWOVERVIEW.
+
+ // I have not determined if this is appropriate for
+ // Jalview/Java, as it means we are setting this flag
+ // for all subsequent AlignFrames. For now, at least,
+ // I am setting it to be JalviewJS-only.
+
+ boolean showAnnotation = Jalview.getInstance().getShowAnnotation();
+ viewport.setShowAnnotation(showAnnotation);
+ }
+ alignPanel = new AlignmentPanel(this, viewport);
+ }
+ addAlignmentPanel(alignPanel, newPanel);
+
// setBackground(Color.white); // BH 2019
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ // JalviewJS options
+ statusPanel.setVisible(Jalview.getInstance().getShowStatus());
+ alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar());
}
avc = new jalview.controller.AlignViewController(this, viewport,
// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ String sortby = jalview.bin.Cache.getDefault(Preferences.SORT_ALIGNMENT,
"No sort");
if (sortby.equals("Id"))
sortPairwiseMenuItem_actionPerformed(null);
}
- this.alignPanel.av
- .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ // BH see above
+ //
+ // this.alignPanel.av
+ // .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
});
buildColourMenu();
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+ addServiceListeners();
if (!Platform.isJS())
{
- addServiceListeners();
}
setGUINucleotide();
}
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ if (jalview.bin.Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
{
this.overviewMenuItem_actionPerformed(null);
}
}
addFocusListener(new FocusAdapter()
{
+
@Override
public void focusGained(FocusEvent e)
{
* @param format
* format of file
*/
+
+ @Deprecated
public void setFileName(String file, FileFormatI format)
{
fileName = file;
}
/**
+ *
+ * @param fileName
+ * @param file from SwingJS; may contain bytes -- for reload
+ * @param protocol from SwingJS; may be RELATIVE_URL
+ * @param format
+ */
+ public void setFile(String fileName, File file, DataSourceType protocol, FileFormatI format)
+ {
+ this.fileName = fileName;
+ this.fileObject = file;
+ this.protocol = protocol;
+ setFileFormat(format);
+ reload.setEnabled(true);
+ }
+
+ /**
* JavaScript will have this, maybe others. More dependable than a file name
* and maintains a reference to the actual bytes loaded.
*
* @param file
*/
+
public void setFileObject(File file)
{
this.fileObject = file;
* Add a KeyListener with handlers for various KeyPressed and KeyReleased
* events
*/
+
void addKeyListener()
{
addKeyListener(new KeyAdapter()
{
+
@Override
public void keyPressed(KeyEvent evt)
{
switch (evt.getKeyCode())
{
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed(null);
+ case KeyEvent.VK_ESCAPE: // escape key
+ // alignPanel.deselectAllSequences();
+ alignPanel.deselectAllSequences();
break;
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
{
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
}
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
{
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
}
break;
}
{
ap.av.getAlignment().padGaps();
}
- ap.av.updateConservation(ap);
- ap.av.updateConsensus(ap);
- ap.av.updateStrucConsensus(ap);
- ap.av.initInformationWorker(ap);
+ if (Jalview.getInstance().getStartCalculations())
+ {
+ ap.av.updateConservation(ap);
+ ap.av.updateConsensus(ap);
+ ap.av.updateStrucConsensus(ap);
++ ap.av.initInformationWorker(ap);
+ }
}
}
return viewport;
}
+ @Override
+ public void servicesChanged(WSDiscovererI discoverer,
+ Collection<? extends ServiceWithParameters> services)
+ {
+ buildWebServicesMenu();
+ }
+
/* Set up intrinsic listeners for dynamically generated GUI bits. */
private void addServiceListeners()
{
- final java.beans.PropertyChangeListener thisListener;
- Desktop.getInstance().addJalviewPropertyChangeListener("services",
- thisListener = new java.beans.PropertyChangeListener()
- {
-
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- // // System.out.println("Discoverer property change.");
- // if (evt.getPropertyName().equals("services"))
- {
- SwingUtilities.invokeLater(new Runnable()
- {
-
- @Override
- public void run()
- {
- System.err.println(
- "Rebuild WS Menu for service change");
- BuildWebServiceMenu();
- }
-
- });
- }
- }
- });
- addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
-
+ WSDiscovererI discoverer = SlivkaWSDiscoverer.getInstance();
+ discoverer.addServiceChangeListener(this);
+ }
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
- WSDiscovererI discoverer = Jws2Discoverer.getDiscoverer();
++ WSDiscovererI discoverer = Jws2Discoverer.getInstance();
+ discoverer.addServiceChangeListener(this);
+ }
+ // legacy event listener for compatibility with jws1
+ PropertyChangeListener legacyListener = (changeEvent) -> {
+ buildWebServicesMenu();
+ };
- Desktop.instance.addJalviewPropertyChangeListener("services",legacyListener);
++ Desktop.getInstance().addJalviewPropertyChangeListener("services",legacyListener);
+
+ addInternalFrameListener(new InternalFrameAdapter() {
@Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- // System.out.println("deregistering discoverer listener");
- Desktop.getInstance().removeJalviewPropertyChangeListener(
- "services", thisListener);
+ public void internalFrameClosed(InternalFrameEvent e) {
+ System.out.println("deregistering discoverer listener");
+ SlivkaWSDiscoverer.getInstance().removeServiceChangeListener(AlignFrame.this);
- Jws2Discoverer.getDiscoverer().removeServiceChangeListener(AlignFrame.this);
- Desktop.instance.removeJalviewPropertyChangeListener("services", legacyListener);
++ Jws2Discoverer.getInstance().removeServiceChangeListener(AlignFrame.this);
++ Desktop.getInstance().removeJalviewPropertyChangeListener("services", legacyListener);
closeMenuItem_actionPerformed(true);
}
});
- // Finally, build the menu once to get current service state
- new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- BuildWebServiceMenu();
- }
- }).start();
+ buildWebServicesMenu();
}
/**
* Configure menu items that vary according to whether the alignment is
* nucleotide or protein
*/
+
public void setGUINucleotide()
{
AlignmentI al = getViewport().getAlignment();
* operation that affects the data in the current view (selection changed,
* etc) to update the menus to reflect the new state.
*/
+
@Override
public void setMenusForViewport()
{
* @param av
* AlignViewport
*/
+
public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
scaleLeft.setVisible(av.getWrapAlignment());
scaleRight.setVisible(av.getWrapAlignment());
annotationPanelMenuItem.setState(av.isShowAnnotation());
- /*
- * Show/hide annotations only enabled if annotation panel is shown
- */
- showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
- showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ // Show/hide annotations only enabled if annotation panel is shown
+ syncAnnotationMenuItems(av.isShowAnnotation());
viewBoxesMenuItem.setSelected(av.getShowBoxes());
viewTextMenuItem.setSelected(av.getShowText());
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+ showInformationHistogram.setSelected(av.isShowInformationHistogram());
+ showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
+ normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
ColourMenuHelper.setColourSelected(colourMenu,
av.getGlobalColourScheme());
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
showDbRefsMenuitem.setSelected(av.isShowDBRefs());
- autoCalculate.setSelected(av.autoCalculateConsensus);
+ autoCalculate
+ .setSelected(av.getAutoCalculateConsensusAndConservation());
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
*
* @param b
*/
+
public void setGroovyEnabled(boolean b)
{
runGroovy.setEnabled(b);
*
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
+
@Override
public void setProgressBar(String message, long id)
{
progressBar.setProgressBar(message, id);
}
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ progressBar.removeProgressBar(id);
+ }
@Override
public void registerHandler(final long id,
*
* @return true if any progress bars are still active
*/
+
@Override
public boolean operationInProgress()
{
* will cause the status bar to be hidden, with possibly undesirable flicker
* of the screen layout.
*/
+
@Override
public void setStatus(String text)
{
/*
* Added so Castor Mapping file can obtain Jalview Version
*/
+
public String getVersion()
{
return jalview.bin.Cache.getProperty("VERSION");
@Override
public void addFromFile_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+ Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport);
}
@Override
+ public void hmmBuild_actionPerformed(boolean withDefaults)
+ {
+ if (!alignmentIsSufficient(1))
+ {
+ return;
+ }
+
+ /*
+ * get default parameters, and optionally show a dialog
+ * to allow them to be modified
+ */
+ ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
+ {
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new HMMBuild(this, args)).start();
+ }
+
+ @Override
+ public void hmmAlign_actionPerformed(boolean withDefaults)
+ {
+ if (!(checkForHMM() && alignmentIsSufficient(2)))
+ {
+ return;
+ }
+
+ /*
+ * get default parameters, and optionally show a dialog
+ * to allow them to be modified
+ */
+ ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
+ {
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new HMMAlign(this, args)).start();
+ }
+
+ @Override
+ public void hmmSearch_actionPerformed(boolean withDefaults)
+ {
+ if (!checkForHMM())
+ {
+ return;
+ }
+
+ /*
+ * get default parameters, and (if requested) show
+ * dialog to allow modification
+ */
+ ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
+ {
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new HMMSearch(this, args)).start();
+ alignPanel.repaint();
+ }
+
+ @Override
+ public void jackhmmer_actionPerformed(boolean withDefaults)
+ {
+
+ /*
+ * get default parameters, and (if requested) show
+ * dialog to allow modification
+ */
+
+ ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
+ {
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new JackHMMER(this, args)).start();
+ alignPanel.repaint();
+
+ }
+
+ /**
+ * Checks if the alignment has at least one hidden Markov model, if not shows
+ * a dialog advising to run hmmbuild or load an HMM profile
+ *
+ * @return
+ */
+ private boolean checkForHMM()
+ {
+ if (viewport.getAlignment().getHmmSequences().isEmpty())
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.no_hmm"));
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ protected void filterByEValue_actionPerformed()
+ {
+ viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
+ }
+
+ @Override
+ protected void filterByScore_actionPerformed()
+ {
+ viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
+ }
+
+ private double inputDouble(String message)
+ {
+ String str = null;
+ Double d = null;
+ while (d == null || d <= 0)
+ {
+ str = JOptionPane.showInputDialog(this.alignPanel, message);
+ try
+ {
+ d = Double.valueOf(str);
+ } catch (NumberFormatException e)
+ {
+ }
+ }
+ return d;
+ }
+
+ /**
+ * Checks if the alignment contains the required number of sequences.
+ *
+ * @param required
+ * @return
+ */
+ public boolean alignmentIsSufficient(int required)
+ {
+ if (getViewport().getSequenceSelection().length < required)
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("label.not_enough_sequences"));
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
+ * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
+ * comma-separated list)
+ */
+ @Override
+ public void addDatabase_actionPerformed() throws IOException
+ {
+ if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
+ {
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+ }
+
+ String path = openFileChooser(false);
+ if (path != null && new File(path).exists())
+ {
+ IdentifyFile identifier = new IdentifyFile();
+ FileFormatI format = identifier.identify(path, DataSourceType.FILE);
+ if (format == FileFormat.Fasta || format == FileFormat.Stockholm
+ || format == FileFormat.Pfam)
+ {
+ String currentDbPaths = Cache
+ .getProperty(Preferences.HMMSEARCH_DBS);
+ currentDbPaths += Preferences.COMMA + path;
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
+ }
+ else
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.invalid_format"));
+ }
+ }
+ }
+
+ /**
+ * Opens a file chooser, optionally restricted to selecting folders
+ * (directories) only. Answers the path to the selected file or folder, or
+ * null if none is chosen.
+ *
+ * @param
+ * @return
+ */
+ protected String openFileChooser(boolean forFolder)
+ {
+ // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
+ String choice = null;
+ JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ choice = chooser.getSelectedFile().getPath();
+ }
+ return choice;
+ }
+
+ @Override
public void reload_actionPerformed(ActionEvent e)
{
- if (fileName != null)
+ if (fileName == null && fileObject == null)
+ {
+ return;
+ }
+ // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+ // originating file's format
+ // TODO: work out how to recover feature settings for correct view(s) when
+ // file is reloaded.
+ if (FileFormat.Jalview.equals(currentFileFormat))
{
- // TODO: JAL-1108 - ensure all associated frames are closed regardless of
- // originating file's format
- // TODO: work out how to recover feature settings for correct view(s) when
- // file is reloaded.
- if (FileFormat.Jalview.equals(currentFileFormat))
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ for (int i = 0; i < frames.length; i++)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- for (int i = 0; i < frames.length; i++)
+ if (frames[i] instanceof AlignFrame && frames[i] != this
+ && ((AlignFrame) frames[i]).fileName != null
+ && ((AlignFrame) frames[i]).fileName.equals(fileName))
{
- if (frames[i] instanceof AlignFrame && frames[i] != this
- && ((AlignFrame) frames[i]).fileName != null
- && ((AlignFrame) frames[i]).fileName.equals(fileName))
+ try
+ {
+ frames[i].setSelected(true);
+ Desktop.getInstance().closeAssociatedWindows();
+ } catch (java.beans.PropertyVetoException ex)
{
- try
- {
- frames[i].setSelected(true);
- Desktop.instance.closeAssociatedWindows();
- } catch (java.beans.PropertyVetoException ex)
- {
- }
}
-
}
- Desktop.instance.closeAssociatedWindows();
- FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE;
- loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
- else
- {
- Rectangle bounds = this.getBounds();
+ Desktop.getInstance().closeAssociatedWindows();
- FileLoader loader = new FileLoader();
+ FileLoader loader = new FileLoader();
+ // DataSourceType protocol = fileName.startsWith("http:")
+ // ? DataSourceType.URL
+ // : DataSourceType.FILE;
+ loader.LoadFile(viewport, (fileObject == null ? fileName : fileObject), protocol, currentFileFormat);
+ }
+ else
+ {
+ Rectangle bounds = this.getBounds();
- AlignFrame newframe = null;
+ FileLoader loader = new FileLoader();
- if (fileObject == null)
- {
+ AlignFrame newframe = null;
- DataSourceType protocol = (fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE);
- newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
- currentFileFormat);
- }
- else
- {
- newframe = loader.LoadFileWaitTillLoaded(fileObject,
- DataSourceType.FILE, currentFileFormat);
- }
+ if (fileObject == null)
+ {
+ newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
+ currentFileFormat);
+ }
+ else
+ {
+ newframe = loader.LoadFileWaitTillLoaded(fileObject,
+ DataSourceType.FILE, currentFileFormat);
+ }
- newframe.setBounds(bounds);
- if (featureSettings != null && featureSettings.isShowing())
+ newframe.setBounds(bounds);
+ if (featureSettings != null && featureSettings.isShowing())
+ {
+ final Rectangle fspos = featureSettings.frame.getBounds();
+ // TODO: need a 'show feature settings' function that takes bounds -
+ // need to refactor Desktop.addFrame
+ newframe.featureSettings_actionPerformed(null);
+ final FeatureSettings nfs = newframe.featureSettings;
+ SwingUtilities.invokeLater(new Runnable()
{
- final Rectangle fspos = featureSettings.frame.getBounds();
- // TODO: need a 'show feature settings' function that takes bounds -
- // need to refactor Desktop.addFrame
- newframe.featureSettings_actionPerformed(null);
- final FeatureSettings nfs = newframe.featureSettings;
- SwingUtilities.invokeLater(new Runnable()
+
+ @Override
+ public void run()
{
- @Override
- public void run()
- {
- nfs.frame.setBounds(fspos);
- }
- });
- this.featureSettings.close();
- this.featureSettings = null;
- }
- this.closeMenuItem_actionPerformed(true);
+ nfs.frame.setBounds(fspos);
+ }
+ });
+ this.featureSettings.close();
+ this.featureSettings = null;
}
+ this.closeMenuItem_actionPerformed(true);
}
+
}
@Override
public void addFromText_actionPerformed(ActionEvent e)
{
- Desktop.instance
+ Desktop.getInstance()
.inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
}
@Override
public void addFromURL_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+ Desktop.getInstance().inputURLMenuItem_actionPerformed(viewport);
}
@Override
* Saves the alignment to a file with a name chosen by the user, if necessary
* warning if a file would be overwritten
*/
+
@Override
public void saveAs_actionPerformed()
{
// todo is this (2005) test now obsolete - value is never null?
while (currentFileFormat == null)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager
.getString("label.select_file_format_before_saving"),
MessageManager.getString("label.file_format_not_specified"),
*
* @return true if last call to saveAlignment(file, format) was successful.
*/
+
public boolean isSaveAlignmentSuccessful()
{
* @param file
* @param format
*/
+
public void saveAlignment(String file, FileFormatI format)
{
lastSaveSuccessful = true;
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
Runnable cancelAction = new Runnable()
{
+
@Override
public void run()
{
};
Runnable outputAction = new Runnable()
{
+
@Override
public void run()
{
*
* @param fileFormatName
*/
+
@Override
protected void outputText_actionPerformed(String fileFormatName)
{
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
Runnable outputAction = new Runnable()
{
+
@Override
public void run()
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
bjs.exportHTML(null);
}
+ // ??
+
public void createImageMap(File file, String image)
{
alignPanel.makePNGImageMap(file, image);
*
* @param f
*/
+
@Override
public void createPNG(File f)
{
*
* @param f
*/
+
@Override
public void createEPS(File f)
{
*
* @param f
*/
+
@Override
public void createSVG(File f)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void printMenuItem_actionPerformed(ActionEvent e)
{
@Override
public void associatedData_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
final JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setToolTipText(tooltip);
chooser.setResponseHandler(0, new Runnable()
{
+
@Override
public void run()
{
*
* @param closeAllTabs
*/
+
@Override
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
*
* @param panelToClose
*/
+
public void closeView(AlignmentPanel panelToClose)
{
int index = tabbedPane.getSelectedIndex();
/**
* DOCUMENT ME!
*/
+
void updateEditMenuBar()
{
*
* @return alignment objects for all views
*/
+
AlignmentI[] getViewAlignments()
{
if (alignPanels != null)
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
// && viewport.getColumnSelection().getHiddenColumns() != null &&
// viewport.getColumnSelection()
// .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null,
- originalSource.getAlignment().getSequences());
+ originalSource.notifyAlignment();
+
}
}
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
// && viewport.getColumnSelection().getHiddenColumns() != null &&
// viewport.getColumnSelection()
// .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null,
- originalSource.getAlignment().getSequences());
+ originalSource.notifyAlignment();
+
}
}
* @param up
* DOCUMENT ME!
*/
+
public void moveSelectedSequences(boolean up)
{
SequenceGroup sg = viewport.getSelectionGroup();
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void copy_actionPerformed()
{
StringSelection ss = new StringSelection(output);
+ Desktop d = Desktop.getInstance();
try
{
- jalview.gui.Desktop.internalCopy = true;
+ d.internalCopy = true;
// Its really worth setting the clipboard contents
// to empty before setting the large StringSelection!!
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(""), null);
Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
- Desktop.instance);
+ Desktop.getInstance());
} catch (OutOfMemoryError er)
{
new OOMWarning("copying region", er);
hiddenCutoff, hiddenOffset);
}
- Desktop.jalviewClipboard = new Object[] { seqs,
+ d.jalviewClipboard = new Object[] { seqs,
viewport.getAlignment().getDataset(), hiddenColumns };
setStatus(MessageManager.formatMessage(
"label.copied_sequences_to_clipboard", new Object[]
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
+
@Override
protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(true);
}
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
+
@Override
protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(false);
}
*
* @param newAlignment
* true to paste to a new alignment, otherwise add to this.
+ * @throws InterruptedException
+ * @throws IOException
*/
-
- void paste(boolean newAlignment)
+ void paste(boolean newAlignment) throws IOException, InterruptedException
{
boolean externalPaste = true;
try
boolean annotationAdded = false;
AlignmentI alignment = null;
- if (Desktop.jalviewClipboard != null)
+ Desktop d = Desktop.getInstance();
+
+ if (d.jalviewClipboard != null)
{
// The clipboard was filled from within Jalview, we must use the
// sequences
// And dataset from the copied alignment
- SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
+ SequenceI[] newseq = (SequenceI[]) d.jalviewClipboard[0];
// be doubly sure that we create *new* sequence objects.
sequences = new SequenceI[newseq.length];
for (int i = 0; i < newseq.length; i++)
if (newAlignment)
{
- if (Desktop.jalviewClipboard != null)
+ if (d.jalviewClipboard != null)
{
// dataset is inherited
- alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
+ alignment.setDataset((Alignment) d.jalviewClipboard[1]);
}
else
{
alignment = viewport.getAlignment();
alwidth = alignment.getWidth() + 1;
// decide if we need to import sequences from an existing dataset
- boolean importDs = Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[1] != alignment.getDataset();
+ boolean importDs = d.jalviewClipboard != null
+ && d.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
}
buildSortByAnnotationScoresMenu();
}
- viewport.firePropertyChange("alignment", null,
- alignment.getSequences());
+ viewport.notifyAlignment();
if (alignPanels != null)
{
for (AlignmentPanel ap : alignPanels)
DEFAULT_HEIGHT);
String newtitle = new String("Copied sequences");
- if (Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[2] != null)
+ if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
{
- HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
System.out.println("Exception whilst pasting: " + ex);
// could be anything being pasted in here
}
-
}
@Override
AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
String newtitle = new String("Flanking alignment");
-
- if (Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[2] != null)
+ Desktop d = Desktop.getInstance();
+ if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
{
- HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
/**
* Action Cut (delete and copy) the selected region
*/
+
@Override
protected void cut_actionPerformed()
{
/**
* Performs menu option to Delete the currently selected region
*/
+
@Override
protected void delete_actionPerformed()
{
Runnable okAction = new Runnable()
{
+
@Override
public void run()
{
viewport.sendSelection();
viewport.getAlignment().deleteGroup(sg);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
+
if (viewport.getAlignment().getHeight() < 1)
{
try
} catch (Exception ex)
{
}
+ } else {
+ updateAll(null);
}
}
};
+ 1) == viewport.getAlignment().getWidth()) ? true : false;
if (wholeHeight && wholeWidth)
{
- JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
+ JvOptionPane dialog = JvOptionPane
+ .newOptionDialog(Desktop.getDesktopPane());
dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
Object[] options = new Object[] {
MessageManager.getString("action.ok"),
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
if (avc.deleteGroups())
{
- PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- alignPanel.updateAnnotation();
+ updateAll(viewport.getSequenceSetId());
+ }
+ }
+
+ private void updateAll(String id)
+ {
+ if (id == null)
+ {
+ // this will force a non-fast repaint of both the IdPanel and SeqPanel
+ alignPanel.getIdPanel().getIdCanvas().setNoFastPaint();
+ alignPanel.getSeqPanel().seqCanvas.setNoFastPaint();
+ alignPanel.repaint();
+ }
+ else
+ {
+ // original version
+ PaintRefresher.Refresh(this, id);
alignPanel.paintAlignment(true, true);
}
+ alignPanel.updateAnnotation();
}
/**
* @param e
* DOCUMENT ME!
*/
+
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- SequenceGroup sg = new SequenceGroup(
- viewport.getAlignment().getSequences());
-
- sg.setEndRes(viewport.getAlignment().getWidth() - 1);
- viewport.setSelectionGroup(sg);
- viewport.isSelectionGroupChanged(true);
- viewport.sendSelection();
- // JAL-2034 - should delegate to
- // alignPanel to decide if overview needs
- // updating.
- alignPanel.paintAlignment(false, false);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ alignPanel.selectAllSequences();
}
/**
* @param e
* DOCUMENT ME!
*/
+
@Override
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- if (viewport.cursorMode)
- {
- alignPanel.getSeqPanel().keyboardNo1 = null;
- alignPanel.getSeqPanel().keyboardNo2 = null;
- }
- viewport.setSelectionGroup(null);
- viewport.getColumnSelection().clear();
- viewport.setSelectionGroup(null);
- alignPanel.getIdPanel().getIdCanvas().searchResults = null;
- // JAL-2034 - should delegate to
- // alignPanel to decide if overview needs
- // updating.
- alignPanel.paintAlignment(false, false);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
+ alignPanel.deselectAllSequences();
}
/**
* @param e
* DOCUMENT ME!
*/
+
@Override
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
if (sg == null)
{
- selectAllSequenceMenuItem_actionPerformed(null);
+ alignPanel.selectAllSequences();
return;
}
* @param e
* DOCUMENT ME!
*/
+
@Override
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
column, viewport.getAlignment());
}
- setStatus(MessageManager
- .formatMessage("label.removed_columns", new String[]
+ setStatus(MessageManager.formatMessage("label.removed_columns",
+ new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
}
}
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
+
}
}
* @param e
* DOCUMENT ME!
*/
+
@Override
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
addHistoryItem(removeGapCols);
- setStatus(MessageManager
- .formatMessage("label.removed_empty_columns", new Object[]
+ setStatus(MessageManager.formatMessage("label.removed_empty_columns",
+ new Object[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
ranges.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
+
}
* @param e
* DOCUMENT ME!
*/
+
@Override
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.getAlignment()));
viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
-
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
}
* @param e
* DOCUMENT ME!
*/
+
@Override
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.setPadGaps(padGapsMenuitem.isSelected());
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
+
}
/**
* @param e
* DOCUMENT ME!
*/
+
@Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
/**
* Create a new view of the current alignment.
*/
+
@Override
public void newView_actionPerformed(ActionEvent e)
{
* if true then duplicate all annnotation, groups and settings
* @return new alignment panel, already displayed.
*/
+
public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
{
/*
if (viewport.getViewName() == null)
{
- viewport.setViewName(MessageManager
- .getString("label.view_name_original"));
+ viewport.setViewName(
+ MessageManager.getString("label.view_name_original"));
}
/*
* @param viewTitle
* @return
*/
+
protected String getNewViewName(String viewTitle)
{
int index = Desktop.getViewCount(viewport.getSequenceSetId());
* @param comps
* @return
*/
+
protected List<String> getExistingViewNames(List<Component> comps)
{
List<String> existingNames = new ArrayList<>();
/**
* Explode tabbed views into separate windows.
*/
+
@Override
public void expandViews_actionPerformed(ActionEvent e)
{
/**
* Gather views in separate windows back into a tabbed presentation.
*/
+
@Override
public void gatherViews_actionPerformed(ActionEvent e)
{
- Desktop.instance.gatherViews(this);
+ Desktop.getInstance().gatherViews(this);
}
/**
* @param e
* DOCUMENT ME!
*/
+
@Override
public void font_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void seqLimit_actionPerformed(ActionEvent e)
{
*
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
+
@Override
protected void followHighlight_actionPerformed()
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
* @param toggleSeqs
* @param toggleCols
*/
+
protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
* jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
* event.ActionEvent)
*/
+
@Override
public void hideAllButSelection_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
* .ActionEvent)
*/
+
@Override
public void hideAllSelection_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
* ActionEvent)
*/
+
@Override
public void showAllhidden_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void scaleAbove_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void scaleLeft_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void scaleRight_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
* @param evt
* DOCUMENT ME!
*/
+
@Override
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
*
* @param e
*/
+
@Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
final boolean setVisible = annotationPanelMenuItem.isSelected();
viewport.setShowAnnotation(setVisible);
- this.showAllSeqAnnotations.setEnabled(setVisible);
- this.hideAllSeqAnnotations.setEnabled(setVisible);
- this.showAllAlAnnotations.setEnabled(setVisible);
- this.hideAllAlAnnotations.setEnabled(setVisible);
+ syncAnnotationMenuItems(setVisible);
alignPanel.updateLayout();
+ repaint();
+ SwingUtilities.invokeLater(new Runnable() {
+
+ @Override
+ public void run()
+ {
+ alignPanel.updateScrollBarsFromRanges();
+ }
+
+ });
+ }
+
+ private void syncAnnotationMenuItems(boolean setVisible)
+ {
+ showAllSeqAnnotations.setEnabled(setVisible);
+ hideAllSeqAnnotations.setEnabled(setVisible);
+ showAllAlAnnotations.setEnabled(setVisible);
+ hideAllAlAnnotations.setEnabled(setVisible);
}
@Override
* @param e
* DOCUMENT ME!
*/
+
@Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
}
JInternalFrame frame = new JInternalFrame();
- final OverviewPanel overview = new OverviewPanel(alignPanel);
+
+ // BH 2019.07.26 we allow for an embedded
+ // undecorated overview with defined size
+ frame.setName(Platform.getAppID("overview"));
+ //
+ Dimension dim = Platform.getDimIfEmbedded(frame, -1, -1);
+ if (dim != null && dim.width == 0)
+ {
+ dim = null; // hidden, not embedded
+ }
+ OverviewPanel overview = new OverviewPanel(alignPanel, dim);
+
frame.setContentPane(overview);
+ if (dim == null)
+ {
+ dim = new Dimension();
+ // was frame.getSize(), but that is 0,0 at this point;
+ }
+ else
+ {
+ // we are imbedding, and so we have an undecorated frame
+ // and we can set the the frame dimensions accordingly.
+ }
+ // allowing for unresizable option using, style="resize:none"
+ boolean resizable = (Platform.getEmbeddedAttribute(frame,
+ "resize") != "none");
Desktop.addInternalFrame(frame, MessageManager
.formatMessage("label.overview_params", new Object[]
- { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
- true, true);
+ { this.getTitle() }), Desktop.FRAME_MAKE_VISIBLE, dim.width,
+ dim.height, resizable, Desktop.FRAME_ALLOW_ANY_SIZE);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
+
@Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
* CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
* ()[0])); }
*/
+
@Override
public void annotationColour_actionPerformed()
{
*
* @param selected
*/
+
@Override
public void applyToAllGroups_actionPerformed(boolean selected)
{
* @param name
* the name (not the menu item label!) of the colour scheme
*/
+
@Override
public void changeColour_actionPerformed(String name)
{
*
* @param cs
*/
+
@Override
public void changeColour(ColourSchemeI cs)
{
/**
* Show the PID threshold slider panel
*/
+
@Override
protected void modifyPID_actionPerformed()
{
/**
* Show the Conservation slider panel
*/
+
@Override
protected void modifyConservation_actionPerformed()
{
/**
* Action on selecting or deselecting (Colour) By Conservation
*/
+
@Override
public void conservationMenuItem_actionPerformed(boolean selected)
{
/**
* Action on selecting or deselecting (Colour) Above PID Threshold
*/
+
@Override
public void abovePIDThreshold_actionPerformed(boolean selected)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
alignPanel.paintAlignment(true, false);
}
+ @Override
+ public void sortEValueMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByEValue(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+
+ @Override
+ public void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByBitScore(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
+
@Override
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
@Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
- viewport.autoCalculateConsensus = autoCalculate.isSelected();
- if (viewport.autoCalculateConsensus)
+ viewport.setAutoCalculateConsensusAndConservation(
+ autoCalculate.isSelected());
+ if (viewport.getAutoCalculateConsensusAndConservation())
+ // ??
+ // viewport.autoCalculateConsensus = autoCalculate.isSelected();
+ // if (viewport.autoCalculateConsensus)
{
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
}
}
* @param options
* parameters for the distance or similarity calculation
*/
+
void newTreePanel(String type, String modelName,
SimilarityParamsI options)
{
{
if (_s.getLength() < sg.getEndRes())
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString(
"label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
MessageManager.getString(
frameTitle += this.title;
- Desktop.addInternalFrame(tp, frameTitle, 600, 500);
+ Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500);
+ Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height);
}
/**
* @param order
* DOCUMENT ME!
*/
+
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
{
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
* the label used to retrieve scores for each sequence on the
* alignment
*/
+
public void addSortByAnnotScoreMenuItem(JMenu sort,
final String scoreLabel)
{
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
* rebuilding in subsequence calls.
*
*/
+
@Override
public void buildSortByAnnotationScoresMenu()
{
}
if (viewport.getAlignment().getAlignmentAnnotation()
- .hashCode() != _annotationScoreVectorHash)
+ .hashCode() == _annotationScoreVectorHash)
+ {
+ return;
+ }
+
+ sortByAnnotScore.removeAll();
+ Set<String> scoreSorts = new HashSet<>();
+ for (SequenceI sqa : viewport.getAlignment().getSequences())
{
- sortByAnnotScore.removeAll();
- // almost certainly a quicker way to do this - but we keep it simple
- Hashtable<String, String> scoreSorts = new Hashtable<>();
- AlignmentAnnotation aann[];
- for (SequenceI sqa : viewport.getAlignment().getSequences())
+ AlignmentAnnotation[] anns = sqa.getAnnotation();
+ for (int i = 0; anns != null && i < anns.length; i++)
{
- aann = sqa.getAnnotation();
- for (int i = 0; aann != null && i < aann.length; i++)
+ AlignmentAnnotation aa = anns[i];
+ if (aa != null && aa.hasScore() && aa.sequenceRef != null)
{
- if (aann[i].hasScore() && aann[i].sequenceRef != null)
- {
- scoreSorts.put(aann[i].label, aann[i].label);
- }
+ scoreSorts.add(aa.label);
}
}
- Enumeration<String> labels = scoreSorts.keys();
- while (labels.hasMoreElements())
- {
- addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
- }
- sortByAnnotScore.setVisible(scoreSorts.size() > 0);
- scoreSorts.clear();
-
- _annotationScoreVectorHash = viewport.getAlignment()
- .getAlignmentAnnotation().hashCode();
}
+ for (String label : scoreSorts)
+ {
+ addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
+ }
+ sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
+
+ _annotationScoreVectorHash = viewport.getAlignment()
+ .getAlignmentAnnotation().hashCode();
}
/**
+ * Enable (or, if desired, make visible) the By Tree
+ * submenu only if it has at least one element (or will have).
+ *
+ */
+ @Override
+ protected void enableSortMenuOptions()
+ {
+ List<TreePanel> treePanels = getTreePanels();
+ sortByTreeMenu.setEnabled(!treePanels.isEmpty());
+ }
+
+ /**
* Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
* TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
* call. Listeners are added to remove the menu item when the treePanel is
* closed, and adjust the tree leaf to sequence mapping when the alignment is
* modified.
*/
+
@Override
public void buildTreeSortMenu()
{
sortByTreeMenu.removeAll();
- List<Component> comps = PaintRefresher.components
- .get(viewport.getSequenceSetId());
- List<TreePanel> treePanels = new ArrayList<>();
- for (Component comp : comps)
- {
- if (comp instanceof TreePanel)
- {
- treePanels.add((TreePanel) comp);
- }
- }
-
- if (treePanels.size() < 1)
- {
- sortByTreeMenu.setVisible(false);
- return;
- }
-
- sortByTreeMenu.setVisible(true);
+ List<TreePanel> treePanels = getTreePanels();
for (final TreePanel tp : treePanels)
{
final JMenuItem item = new JMenuItem(tp.getTitle());
item.addActionListener(new java.awt.event.ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
}
}
+ private List<TreePanel> getTreePanels()
+ {
+ List<Component> comps = PaintRefresher.components
+ .get(viewport.getSequenceSetId());
+ List<TreePanel> treePanels = new ArrayList<>();
+ for (Component comp : comps)
+ {
+ if (comp instanceof TreePanel)
+ {
+ treePanels.add((TreePanel) comp);
+ }
+ }
+ return treePanels;
+ }
+
public boolean sortBy(AlignmentOrder alorder, String undoname)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
* be submitted for multiple alignment.
*
*/
+
public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
{
// Now, check we have enough sequences
* region or the whole alignment. (where the first sequence in the set is the
* one that the prediction will be for).
*/
+
public AlignmentView gatherSeqOrMsaForSecStrPrediction()
{
AlignmentView seqs = null;
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
chooser.setResponseHandler(0, new Runnable()
{
+
@Override
public void run()
{
viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
{
- JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+ ex.getMessage(),
MessageManager
.getString("label.problem_reading_tree_file"),
JvOptionPane.WARNING_MESSAGE);
}
if (fin != null && fin.hasWarningMessage())
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
fin.getWarningMessage(),
MessageManager.getString(
"label.possible_problem_with_tree_file"),
* position
* @return TreePanel handle
*/
+
public TreePanel showNewickTree(NewickFile nf, String treeTitle,
AlignmentView input, int w, int h, int x, int y)
{
if (nf.getTree() != null)
{
tp = new TreePanel(alignPanel, nf, treeTitle, input);
-
- tp.setSize(w, h);
+ Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1);
+ if (dim == null)
+ {
+ dim = new Dimension(w, h);
+ }
+ else
+ {
+ // no offset, either
+ x = 0;
+ }
+ tp.setSize(dim.width, dim.height);
if (x > 0 && y > 0)
{
tp.setLocation(x, y);
}
- Desktop.addInternalFrame(tp, treeTitle, w, h);
+ Desktop.addInternalFrame(tp, treeTitle, dim.width, dim.height);
}
} catch (Exception ex)
{
return tp;
}
- private boolean buildingMenu = false;
-
/**
- * Generates menu items and listener event actions for web service clients
- *
+ * Schedule the web services menu rebuild to the event dispatch thread.
*/
-
- public void BuildWebServiceMenu()
+ public void buildWebServicesMenu()
{
- while (buildingMenu)
- {
- try
+ SwingUtilities.invokeLater(() -> {
+ Cache.log.info("Rebuiling WS menu");
+ webService.removeAll();
+ if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
- System.err.println("Waiting for building menu to finish.");
- Thread.sleep(10);
- } catch (Exception e)
+ Cache.log.info("Building web service menu for slivka");
+ SlivkaWSDiscoverer discoverer = SlivkaWSDiscoverer.getInstance();
+ JMenu submenu = new JMenu("Slivka");
+ buildWebServicesMenu(discoverer, submenu);
+ webService.add(submenu);
+ }
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- WSDiscovererI jws2servs = Jws2Discoverer.getDiscoverer();
++ WSDiscovererI jws2servs = Jws2Discoverer.getInstance();
+ JMenu submenu = new JMenu("JABAWS");
+ buildLegacyWebServicesMenu(submenu);
+ buildWebServicesMenu(jws2servs, submenu);
+ webService.add(submenu);
}
- }
- final AlignFrame me = this;
- buildingMenu = true;
- new Thread(new Runnable()
- {
+ });
+ }
- @Override
- public void run()
+ private void buildLegacyWebServicesMenu(JMenu menu)
+ {
+ JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
- if (Discoverer.services != null && Discoverer.services.size() > 0)
++ if (Discoverer.getServices() != null && Discoverer.getServices().size() > 0)
+ {
- var secstrpred = Discoverer.services.get("SecStrPred");
++ var secstrpred = Discoverer.getServices().get("SecStrPred");
+ if (secstrpred != null)
{
- final List<JMenuItem> legacyItems = new ArrayList<>();
- try
- {
- // System.err.println("Building ws menu again "
- // + Thread.currentThread());
- // TODO: add support for context dependent disabling of services based
- // on
- // alignment and current selection
- // TODO: add additional serviceHandle parameter to specify abstract
- // handler
- // class independently of AbstractName
- // TODO: add in rediscovery GUI function to restart discoverer
- // TODO: group services by location as well as function and/or
- // introduce
- // object broker mechanism.
- final Vector<JMenu> wsmenu = new Vector<>();
- final IProgressIndicator af = me;
-
- /*
- * do not i18n these strings - they are hard-coded in class
- * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
- * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
- */
- final JMenu msawsmenu = new JMenu("Alignment");
- final JMenu secstrmenu = new JMenu(
- "Secondary Structure Prediction");
- final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- final JMenu analymenu = new JMenu("Analysis");
- final JMenu dismenu = new JMenu("Protein Disorder");
- // JAL-940 - only show secondary structure prediction services from
- // the legacy server
- Hashtable<String, Vector<ServiceHandle>> ds = Discoverer
- .getInstance().getServices();
- if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
- // &&
- ds != null && (ds.size() > 0))
- {
- // TODO: refactor to allow list of AbstractName/Handler bindings to
- // be
- // stored or retrieved from elsewhere
- // No MSAWS used any more:
- // Vector msaws = null; // (Vector)
- // Discoverer.services.get("MsaWS");
- Vector<ServiceHandle> secstrpr = ds.get("SecStrPred");
- if (secstrpr != null)
- {
- // Add any secondary structure prediction services
- for (int i = 0, j = secstrpr.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- int p = secstrmenu.getItemCount();
- impl.attachWSMenuEntry(secstrmenu, me);
- int q = secstrmenu.getItemCount();
- for (int litm = p; litm < q; litm++)
- {
- legacyItems.add(secstrmenu.getItem(litm));
- }
- }
- }
- }
-
- // Add all submenus in the order they should appear on the web
- // services menu
- wsmenu.add(msawsmenu);
- wsmenu.add(secstrmenu);
- wsmenu.add(dismenu);
- wsmenu.add(analymenu);
- // No search services yet
- // wsmenu.add(seqsrchmenu);
-
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
-
- @Override
- public void run()
- {
- try
- {
- webService.removeAll();
- // first, add discovered services onto the webservices menu
- if (wsmenu.size() > 0)
- {
- for (int i = 0, j = wsmenu.size(); i < j; i++)
- {
- webService.add(wsmenu.get(i));
- }
- }
- else
- {
- webService.add(me.webServiceNoServices);
- }
- // TODO: move into separate menu builder class.
- // boolean new_sspred = false;
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
- {
- Jws2Discoverer jws2servs = Jws2Discoverer.getInstance();
- if (jws2servs != null)
- {
- if (jws2servs.hasServices())
- {
- jws2servs.attachWSMenuEntry(webService, me);
- for (Jws2Instance sv : jws2servs.getServices())
- {
- if (sv.description.toLowerCase().contains("jpred"))
- {
- for (JMenuItem jmi : legacyItems)
- {
- jmi.setVisible(false);
- }
- }
- }
-
- }
- if (jws2servs.isRunning())
- {
- JMenuItem tm = new JMenuItem(
- "Still discovering JABA Services");
- tm.setEnabled(false);
- webService.add(tm);
- }
- }
- }
- build_urlServiceMenu(me.webService);
- build_fetchdbmenu(webService);
- for (JMenu item : wsmenu)
- {
- if (item.getItemCount() == 0)
- {
- item.setEnabled(false);
- }
- else
- {
- item.setEnabled(true);
- }
- }
- } catch (Exception e)
- {
- Cache.log.debug(
- "Exception during web service menu building process.",
- e);
- }
- }
- });
- } catch (Exception e)
+ for (ext.vamsas.ServiceHandle sh : secstrpred)
{
+ var menuProvider = Discoverer.getServiceClient(sh);
+ menuProvider.attachWSMenuEntry(secstrmenu, this);
}
- buildingMenu = false;
}
- }).start();
+ }
+ menu.add(secstrmenu);
+ }
+ /**
+ * Constructs the web services menu for the given discoverer under the
+ * specified menu. This method must be called on the EDT
+ *
+ * @param discoverer
+ * the discoverer used to build the menu
+ * @param menu
+ * parent component which the elements will be attached to
+ */
+ private void buildWebServicesMenu(WSDiscovererI discoverer, JMenu menu)
+ {
+ if (discoverer.hasServices())
+ {
+ PreferredServiceRegistry.getRegistry().populateWSMenuEntry(
+ discoverer.getServices(), sv -> buildWebServicesMenu(), menu,
+ this, null);
+ }
+ if (discoverer.isRunning())
+ {
+ JMenuItem item = new JMenuItem("Service discovery in progress.");
+ item.setEnabled(false);
+ menu.add(item);
+ }
+ else if (!discoverer.hasServices())
+ {
+ JMenuItem item = new JMenuItem("No services available.");
+ item.setEnabled(false);
+ menu.add(item);
+ }
}
/**
*
* @param webService
*/
+
protected void build_urlServiceMenu(JMenu webService)
{
// TODO: remove this code when 2.7 is released
* JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
* AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
*
- * @Override public void actionPerformed(ActionEvent e) {
+ * public void actionPerformed(ActionEvent e) {
* jalview.datamodel.AlignmentView
* .testSelectionViews(af.viewport.getAlignment(),
* af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
*
* @return true if Show Cross-references menu should be enabled
*/
+
public boolean canShowProducts()
{
SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
JMenuItem xtype = new JMenuItem(source);
xtype.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
* @param source
* the database to show cross-references for
*/
+
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
* Construct and display a new frame containing the translation of this
* frame's DNA sequences to their aligned protein (amino acid) equivalents.
*/
+
@Override
public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("label.translation_failed");
- JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
- JvOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg,
+ errorTitle, JvOptionPane.ERROR_MESSAGE);
return;
}
if (al == null || al.getHeight() == 0)
"label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
final String errorTitle = MessageManager
.getString("label.translation_failed");
- JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg,
+ errorTitle, JvOptionPane.WARNING_MESSAGE);
}
else
{
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
- viewport.openSplitFrame(af, new Alignment(seqs));
+ AlignViewport.openSplitFrame(this, af, new Alignment(seqs));
}
else
{
*
* @param format
*/
+
public void setFileFormat(FileFormatI format)
{
this.currentFileFormat = format;
* access mode of file (see jalview.io.AlignFile)
* @return true if features file was parsed correctly.
*/
+
public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
{
// BH 2018
return avc.parseFeaturesFile(file, sourceType,
- Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+ Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false));
}
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
- final AlignFrame thisaf = this;
final List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
try
{
Desktop.transferFromDropTarget(files, protocols, evt, t);
+ if (files.size() > 0)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ loadDroppedFiles(files, protocols, evt, t);
+ }
+ }).start();
+ }
} catch (Exception e)
{
e.printStackTrace();
}
- if (files != null)
+ }
+
+ protected void loadDroppedFiles(List<Object> files,
+ List<DataSourceType> protocols, DropTargetDropEvent evt,
+ Transferable t)
+ {
+ try
{
- new Thread(new Runnable()
+ // check to see if any of these files have names matching sequences
+ // in
+ // the alignment
+ SequenceIdMatcher idm = new SequenceIdMatcher(
+ viewport.getAlignment().getSequencesArray());
+ /**
+ * Object[] { String,SequenceI}
+ */
+ ArrayList<Object[]> filesmatched = new ArrayList<>();
+ ArrayList<Object> filesnotmatched = new ArrayList<>();
+ for (int i = 0; i < files.size(); i++)
{
- @Override
- public void run()
+ // BH 2018
+ Object fileObj = files.get(i);
+ String fileName = fileObj.toString();
+ String pdbfn = "";
+ DataSourceType protocol = (fileObj instanceof File
+ ? DataSourceType.FILE
+ : FormatAdapter.checkProtocol(fileName));
+ if (protocol == DataSourceType.FILE)
{
- try
+ File file;
+ if (fileObj instanceof File)
+ {
+ file = (File) fileObj;
+ Platform.cacheFileData(file);
+ }
+ else
{
- // check to see if any of these files have names matching sequences
- // in
- // the alignment
- SequenceIdMatcher idm = new SequenceIdMatcher(
- viewport.getAlignment().getSequencesArray());
- /**
- * Object[] { String,SequenceI}
- */
- ArrayList<Object[]> filesmatched = new ArrayList<>();
- ArrayList<Object> filesnotmatched = new ArrayList<>();
- for (int i = 0; i < files.size(); i++)
+ file = new File(fileName);
+ }
+ pdbfn = file.getName();
+ }
+ else if (protocol == DataSourceType.URL)
+ {
+ URL url = new URL(fileName);
+ pdbfn = url.getFile();
+ }
+ if (pdbfn.length() > 0)
+ {
+ // attempt to find a match in the alignment
+ SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
+ int l = 0, c = pdbfn.indexOf(".");
+ while (mtch == null && c != -1)
+ {
+ do
{
- // BH 2018
- Object file = files.get(i);
- String fileName = file.toString();
- String pdbfn = "";
- DataSourceType protocol = (file instanceof File
- ? DataSourceType.FILE
- : FormatAdapter.checkProtocol(fileName));
- if (protocol == DataSourceType.FILE)
- {
- File fl;
- if (file instanceof File)
- {
- fl = (File) file;
- Platform.cacheFileData(fl);
- }
- else
- {
- fl = new File(fileName);
- }
- pdbfn = fl.getName();
- }
- else if (protocol == DataSourceType.URL)
- {
- URL url = new URL(fileName);
- pdbfn = url.getFile();
- }
- if (pdbfn.length() > 0)
- {
- // attempt to find a match in the alignment
- SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
- int l = 0, c = pdbfn.indexOf(".");
- while (mtch == null && c != -1)
- {
- do
- {
- l = c;
- } while ((c = pdbfn.indexOf(".", l)) > l);
- if (l > -1)
- {
- pdbfn = pdbfn.substring(0, l);
- }
- mtch = idm.findAllIdMatches(pdbfn);
- }
- if (mtch != null)
- {
- FileFormatI type;
- try
- {
- type = new IdentifyFile().identify(file, protocol);
- } catch (Exception ex)
- {
- type = null;
- }
- if (type != null && type.isStructureFile())
- {
- filesmatched.add(new Object[] { file, protocol, mtch });
- continue;
- }
- }
- // File wasn't named like one of the sequences or wasn't a PDB
- // file.
- filesnotmatched.add(file);
- }
+ l = c;
+ } while ((c = pdbfn.indexOf(".", l)) > l);
+ if (l > -1)
+ {
+ pdbfn = pdbfn.substring(0, l);
}
- int assocfiles = 0;
- if (filesmatched.size() > 0)
+ mtch = idm.findAllIdMatches(pdbfn);
+ }
+ if (mtch != null)
+ {
+ FileFormatI type;
+ try
{
- boolean autoAssociate = Cache
- .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
- if (!autoAssociate)
- {
- String msg = MessageManager.formatMessage(
- "label.automatically_associate_structure_files_with_sequences_same_name",
- new Object[]
- { Integer.valueOf(filesmatched.size())
- .toString() });
- String ttl = MessageManager.getString(
- "label.automatically_associate_structure_files_by_name");
- int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
- ttl, JvOptionPane.YES_NO_OPTION);
- autoAssociate = choice == JvOptionPane.YES_OPTION;
- }
- if (autoAssociate)
- {
- for (Object[] fm : filesmatched)
- {
- // try and associate
- // TODO: may want to set a standard ID naming formalism for
- // associating PDB files which have no IDs.
- for (SequenceI toassoc : (SequenceI[]) fm[2])
- {
- PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(fm[0].toString(),
- (DataSourceType) fm[1], toassoc, false,
- Desktop.instance);
- if (pe != null)
- {
- System.err.println("Associated file : "
- + (fm[0].toString()) + " with "
- + toassoc.getDisplayId(true));
- assocfiles++;
- }
- }
- // TODO: do we need to update overview ? only if features are
- // shown I guess
- alignPanel.paintAlignment(true, false);
- }
- }
- else
- {
- /*
- * add declined structures as sequences
- */
- for (Object[] o : filesmatched)
- {
- filesnotmatched.add(o[0]);
- }
- }
+ type = new IdentifyFile().identify(fileObj, protocol);
+ } catch (Exception ex)
+ {
+ type = null;
}
- if (filesnotmatched.size() > 0)
+ if (type != null && type.isStructureFile())
{
- if (assocfiles > 0 && (Cache.getDefault(
- "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
- || JvOptionPane.showConfirmDialog(thisaf,
- "<html>" + MessageManager.formatMessage(
- "label.ignore_unmatched_dropped_files_info",
- new Object[]
- { Integer.valueOf(
- filesnotmatched.size())
- .toString() })
- + "</html>",
- MessageManager.getString(
- "label.ignore_unmatched_dropped_files"),
- JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
- {
- return;
- }
- for (Object fn : filesnotmatched)
+ filesmatched.add(new Object[] { fileObj, protocol, mtch });
+ continue;
+ }
+ }
+ // File wasn't named like one of the sequences or wasn't a PDB
+ // file.
+ filesnotmatched.add(fileObj);
+ }
+ }
+ int assocfiles = 0;
+ if (filesmatched.size() > 0)
+ {
+ boolean autoAssociate = Cache
+ .getDefault(Preferences.AUTOASSOCIATE_PDBANDSEQS, false);
+ if (!autoAssociate)
+ {
+ String msg = MessageManager.formatMessage(
+ "label.automatically_associate_structure_files_with_sequences_same_name",
+ new Object[]
+ { Integer.valueOf(filesmatched.size()).toString() });
+ String ttl = MessageManager.getString(
+ "label.automatically_associate_structure_files_by_name");
+ int choice = JvOptionPane.showConfirmDialog(this, msg, ttl,
+ JvOptionPane.YES_NO_OPTION);
+ autoAssociate = choice == JvOptionPane.YES_OPTION;
+ }
+ if (autoAssociate)
+ {
+ for (Object[] fm : filesmatched)
+ {
+ // try and associate
+ // TODO: may want to set a standard ID naming formalism for
+ // associating PDB files which have no IDs.
+ for (SequenceI toassoc : (SequenceI[]) fm[2])
+ {
+ PDBEntry pe = AssociatePdbFileWithSeq.associatePdbWithSeq(
+ fm[0].toString(), (DataSourceType) fm[1], toassoc,
+ false);
+ if (pe != null)
{
- loadJalviewDataFile(fn, null, null, null);
+ System.err.println("Associated file : " + (fm[0].toString())
+ + " with " + toassoc.getDisplayId(true));
+ assocfiles++;
}
-
}
- } catch (Exception ex)
+ // TODO: do we need to update overview ? only if features are
+ // shown I guess
+ alignPanel.paintAlignment(true, false);
+ }
+ }
+ else
+ {
+ /*
+ * add declined structures as sequences
+ */
+ for (Object[] o : filesmatched)
{
- ex.printStackTrace();
+ filesnotmatched.add(o[0]);
}
}
- }).start();
+ }
+ if (filesnotmatched.size() > 0)
+ {
+ if (assocfiles > 0 && (Cache
+ .getDefault("AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
+ || JvOptionPane.showConfirmDialog(this,
+ "<html>" + MessageManager.formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new Object[]
+ { Integer.valueOf(filesnotmatched.size())
+ .toString() })
+ + "</html>",
+ MessageManager.getString(
+ "label.ignore_unmatched_dropped_files"),
+ JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
+ {
+ return;
+ }
+ for (Object fn : filesnotmatched)
+ {
+ loadJalviewDataFile(fn, null, null, null);
+ }
+
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
}
*
* @param file
* either a filename or a URL string.
+ * @throws InterruptedException
+ * @throws IOException
*/
+
public void loadJalviewDataFile(Object file, DataSourceType sourceType,
FileFormatI format, SequenceI assocSeq)
{
{
// some problem - if no warning its probable that the ID matching
// process didn't work
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
tcf.getWarningMessage() == null
? MessageManager.getString(
"label.check_file_matches_sequence_ids_alignment")
}
if (isAnnotation)
{
- alignPanel.adjustAnnotationHeight();
- viewport.updateSequenceIdColours();
- buildSortByAnnotationScoresMenu();
- alignPanel.paintAlignment(true, true);
+ updateForAnnotations();
}
} catch (Exception ex)
{
+ (format != null
? "(parsing as '" + format + "' file)"
: ""),
- oom, Desktop.desktop);
+ oom, Desktop.getDesktopPane());
+ }
+ }
+
+ /**
+ * Do all updates necessary after an annotation file such as jnet. Also called
+ * from Jalview.loadAppletParams for "annotations", "jnetFile"
+ */
+
+ public void updateForAnnotations()
+ {
+ alignPanel.adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ buildSortByAnnotationScoresMenu();
+ alignPanel.paintAlignment(true, true);
+ }
+
+ /**
+ * Change the display state for the given feature groups -- Added by BH from
+ * JalviewLite
+ *
+ * @param groups
+ * list of group strings
+ * @param state
+ * visible or invisible
+ */
+
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ jalview.api.FeatureRenderer fr = null;
+ viewport.setShowSequenceFeatures(true);
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+
+ fr.setGroupVisibility(Arrays.asList(groups), state);
+ alignPanel.getSeqPanel().seqCanvas.repaint();
+ if (alignPanel.overviewPanel != null)
+ {
+ alignPanel.overviewPanel.updateOverviewImage();
+ }
}
}
* Method invoked by the ChangeListener on the tabbed pane, in other words
* when a different tabbed pane is selected by the user or programmatically.
*/
+
@Override
public void tabSelectionChanged(int index)
{
/**
* On right mouse click on view tab, prompt for and set new view name.
*/
+
@Override
public void tabbedPane_mousePressed(MouseEvent e)
{
/**
* Open the dialog for regex description parsing.
*/
+
@Override
protected void extractScores_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
* )
*/
+
@Override
protected void showDbRefs_actionPerformed(ActionEvent e)
{
* @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
* ActionEvent)
*/
+
@Override
protected void showNpFeats_actionPerformed(ActionEvent e)
{
*
* @param av
*/
+
public boolean closeView(AlignViewportI av)
{
if (viewport == av)
Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
trimrs.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
{
new Thread(new Runnable()
{
+
@Override
public void run()
{
alignPanel.alignFrame.featureSettings, isNucleotide);
dbRefFetcher.addListener(new FetchFinishedListenerI()
{
+
@Override
public void finished()
{
rfetch.add(fetchr);
new Thread(new Runnable()
{
+
@Override
public void run()
{
- final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
- .getSequenceFetcherSingleton();
+ // ??
+ // final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
+ // .getSequenceFetcherSingleton();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+
@Override
public void run()
{
+ jalview.ws.SequenceFetcher sf = jalview.ws.SequenceFetcher
+ .getInstance();
String[] dbclasses = sf.getNonAlignmentSources();
List<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
}
if (otherdb.size() == 1)
{
- final DbSourceProxy[] dassource = otherdb
- .toArray(new DbSourceProxy[0]);
DbSourceProxy src = otherdb.get(0);
+ DbSourceProxy[] dassource = new DbSourceProxy[] { src };
fetchr = new JMenuItem(src.getDbSource());
fetchr.addActionListener(new ActionListener()
{
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
+
@Override
public void finished()
{
{ src.getDbSource() }));
fetchr.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
+
@Override
public void finished()
{
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
+
@Override
public void finished()
{
/**
* Left justify the whole alignment.
*/
+
@Override
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
- AlignmentI al = viewport.getAlignment();
- al.justify(false);
- viewport.firePropertyChange("alignment", null, al);
+ viewport.getAlignment().justify(false);
+ viewport.notifyAlignment();
}
/**
* Right justify the whole alignment.
*/
+
@Override
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
- AlignmentI al = viewport.getAlignment();
- al.justify(true);
- viewport.firePropertyChange("alignment", null, al);
+ viewport.getAlignment().justify(true);
+ viewport.notifyAlignment();
}
@Override
* jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
* awt.event.ActionEvent)
*/
+
@Override
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
* .ActionEvent)
*/
+
@Override
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
* .event.ActionEvent)
*/
+
@Override
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
*/
+
@Override
protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
*/
+
@Override
protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
* .event.ActionEvent)
*/
+
@Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
*
* @param alignmentPanel
*/
+
public void setDisplayedView(AlignmentPanel alignmentPanel)
{
if (!viewport.getSequenceSetId()
* @param forAlignment
* update non-sequence-related annotations
*/
+
@Override
protected void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
/**
* Store selected annotation sort order for the view and repaint.
*/
+
@Override
protected void sortAnnotations_actionPerformed()
{
*
* @return alignment panels in this alignment frame
*/
+
public List<? extends AlignmentViewPanel> getAlignPanels()
{
// alignPanels is never null
* Open a new alignment window, with the cDNA associated with this (protein)
* alignment, aligned as is the protein.
*/
+
protected void viewAsCdna_actionPerformed()
{
// TODO no longer a menu action - refactor as required
*
* @param show
*/
+
@Override
protected void showComplement_actionPerformed(boolean show)
{
* Generate the reverse (optionally complemented) of the selected sequences,
* and add them to the alignment
*/
+
@Override
protected void showReverse_actionPerformed(boolean complement)
{
* AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
* be targeted at this alignment.
*/
+
@Override
protected void runGroovy_actionPerformed()
{
} catch (Exception ex)
{
System.err.println((ex.toString()));
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.couldnt_run_groovy_script"),
MessageManager.getString("label.groovy_support_failed"),
JvOptionPane.ERROR_MESSAGE);
* @param columnsContaining
* @return
*/
+
public boolean hideFeatureColumns(String featureType,
boolean columnsContaining)
{
* Rebuilds the Colour menu, including any user-defined colours which have
* been loaded either on startup or during the session
*/
+
public void buildColourMenu()
{
colourMenu.removeAll();
* Open a dialog (if not already open) that allows the user to select and
* calculate PCA or Tree analysis
*/
+
protected void openTreePcaDialog()
{
if (alignPanel.getCalculationDialog() == null)
}
}
+ /**
+ * Sets the status of the HMMER menu
+ */
+ public void updateHMMERStatus()
+ {
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+ }
+
@Override
protected void loadVcf_actionPerformed()
{
final AlignFrame us = this;
chooser.setResponseHandler(0, new Runnable()
{
+
@Override
public void run()
{
{
return lastFeatureSettingsBounds;
}
- }
- class PrintThread extends Thread
- {
- AlignmentPanel ap;
+ public void scrollTo(int row, int column)
+ {
+ alignPanel.getSeqPanel().scrollTo(row, column);
+ }
- public PrintThread(AlignmentPanel ap)
+ public void scrollToRow(int row)
{
- this.ap = ap;
+ alignPanel.getSeqPanel().scrollToRow(row);
}
- static PageFormat pf;
+ public void scrollToColumn(int column)
+ {
+ alignPanel.getSeqPanel().scrollToColumn(column);
+ }
- @Override
- public void run()
+ /**
+ * BH 2019 from JalviewLite
+ *
+ * get sequence feature groups that are hidden or shown
+ *
+ * @param visible
+ * true is visible
+ * @return list
+ */
+
+ public String[] getFeatureGroupsOfState(boolean visible)
{
- PrinterJob printJob = PrinterJob.getPrinterJob();
+ jalview.api.FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getGroups(visible);
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ return null;
+ }
- if (pf != null)
+ /**
+ *
+ * @return list of feature groups on the view
+ */
+
+ public String[] getFeatureGroups()
+ {
+ jalview.api.FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
{
- printJob.setPrintable(ap, pf);
+ List<String> gps = fr.getFeatureGroups();
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
}
- else
+ return null;
+ }
+
+ public void select(SequenceGroup sel, ColumnSelection csel,
+ HiddenColumns hidden)
+ {
+ alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
+ }
+
+ public int getID()
+ {
+ return id;
+ }
+
+ static class PrintThread extends Thread
+ {
+ AlignmentPanel ap;
+
+ public PrintThread(AlignmentPanel ap)
{
- printJob.setPrintable(ap);
+ this.ap = ap;
}
- if (printJob.printDialog())
+ static PageFormat pf;
+
+ @Override
+ public void run()
{
- try
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+
+ if (pf != null)
{
- printJob.print();
- } catch (Exception PrintException)
+ printJob.setPrintable(ap, pf);
+ }
+ else
+ {
+ printJob.setPrintable(ap);
+ }
+
+ if (printJob.printDialog())
{
- PrintException.printStackTrace();
+ try
+ {
+ printJob.print();
+ } catch (Exception PrintException)
+ {
+ PrintException.printStackTrace();
+ }
}
}
}
}
+
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
public class AlignViewport extends AlignmentViewport
implements SelectionSource
{
+
+ public final static int NO_SPLIT = 0;
+
+ public final static int SPLIT_FRAME = 1;
+
+ public final static int NEW_WINDOW = 2;
+
+
Font font;
boolean cursorMode = false;
* @param hiddenColumns
* @param seqsetid
* (may be null)
- */
+ f */
public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
String seqsetid)
{
setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
- autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+ autoCalculateConsensusAndConservation = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
setPadGaps(Cache.getDefault("PAD_GAPS", true));
setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
- alignment
- .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+ alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
- if (hconsensus == null && !isDataset)
+ if (hconsensus == null && !isDataset)
{
- if (!alignment.isNucleotide())
+ if (!alignment.isNucleotide())
{
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
showQuality = Cache.getDefault("SHOW_QUALITY", true);
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
false);
+ // for now, use consensus options for Information till it gets its own
+ setShowHMMSequenceLogo(showSequenceLogo);
+ setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
+ setShowInformationHistogram(showConsensusHistogram);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
- String colourProperty = alignment.isNucleotide()
+ // initInformation();
+
+ String colourProperty = alignment.isNucleotide()
? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
String schemeName = Cache.getProperty(colourProperty);
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(hconsensus);
}
setColourAppliesToAllGroups(true);
}
-
+
boolean validCharWidth;
/**
if (align != null)
{
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.registerMappings(align.getCodonFrames());
}
/*
* replace mappings on our alignment
*/
- if (alignment != null && align != null)
+ if (alignment != null && align != null)
{
alignment.setCodonFrames(align.getCodonFrames());
}
if (mappings != null)
{
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
for (AlignedCodonFrame acf : mappings)
{
if (noReferencesTo(acf))
}
/**
- * returns the visible column regions of the alignment
+ * Returns an iterator over the visible column regions of the alignment
*
* @param selectedRegionOnly
* true to just return the contigs intersecting with the selected
{
end = alignment.getWidth();
}
- return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
- false));
+
+ return (alignment.getHiddenColumns().getVisContigsIterator(start,
+ end, false));
}
/**
}
public boolean followSelection = true;
-
+
/**
* @return true if view selection should always follow the selections
* broadcast by other selection sources
public void sendSelection()
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Desktop.getInstance())
.sendSelection(new SequenceGroup(getSelectionGroup()),
new ColumnSelection(getColumnSelection()),
new HiddenColumns(getAlignment().getHiddenColumns()),
public StructureSelectionManager getStructureSelectionManager()
{
return StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
}
-
+
@Override
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
}
- public void setNormaliseSequenceLogo(boolean state)
+ @Override
+public void setNormaliseSequenceLogo(boolean state)
{
normaliseSequenceLogo = state;
}
+
/**
*
* @return true if alignment characters should be displayed
{
return validCharWidth;
}
-
+
private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
}
ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
- firePropertyChange("alignment", null, getAlignment().getSequences());
+ notifyAlignment();
+
}
/**
* dialog responses 0, 1, 2 (even though JOptionPane shows them
* in reverse order)
*/
- JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
- .setResponseHandler(0, new Runnable()
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane())
+ .setResponseHandler(NO_SPLIT, new Runnable()
{
@Override
public void run()
{
addDataToAlignment(al);
}
- }).setResponseHandler(1, new Runnable()
+ }).setResponseHandler(SPLIT_FRAME, new Runnable()
{
@Override
public void run()
{
- us.openLinkedAlignmentAs(al, title, true);
+ openLinkedAlignmentAs(getAlignPanel().alignFrame,
+ new Alignment(getAlignment()), al, title,
+ SPLIT_FRAME);
+ // us.openLinkedAlignmentAs(al, title, true);
}
- }).setResponseHandler(2, new Runnable()
+ }).setResponseHandler(NEW_WINDOW, new Runnable()
{
@Override
public void run()
{
- us.openLinkedAlignmentAs(al, title, false);
+ openLinkedAlignmentAs(null, getAlignment(), al, title,
+ NEW_WINDOW);
}
});
- dialog.showDialog(question,
+ dialog.showDialog(question,
MessageManager.getString("label.open_split_window"),
JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
}
-
- protected void openLinkedAlignmentAs(AlignmentI al, String title,
- boolean newWindowOrSplitPane)
- {
+ /**
+ * Open a split frame or a new window
+ *
+ * @param al
+ * @param title
+ * @param mode
+ * SPLIT_FRAME or NEW_WINDOW
+ */
+ public static void openLinkedAlignmentAs(AlignFrame thisFrame,
+ AlignmentI thisAlignment, AlignmentI al, String title, int mode)
+ {
/*
* Identify protein and dna alignments. Make a copy of this one if opening
* in a new split pane.
*/
- AlignmentI thisAlignment = newWindowOrSplitPane
- ? new Alignment(getAlignment())
- : getAlignment();
AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
- final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
-
+ AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
/*
* Map sequences. At least one should get mapped as we have already passed
* the test for 'mappability'. Any mappings made will be added to the
// alignFrame.setFileName(file, format);
// }
- if (!newWindowOrSplitPane)
+ if (mode == NEW_WINDOW)
{
Desktop.addInternalFrame(newAlignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
{
}
- if (newWindowOrSplitPane)
+ if (mode == SPLIT_FRAME)
{
al.alignAs(thisAlignment);
- protein = openSplitFrame(newAlignFrame, thisAlignment);
+ openSplitFrame(thisFrame, newAlignFrame, thisAlignment);
}
}
* cdna/protein complement alignment to show in the other split half
* @return the protein alignment in the split frame
*/
- protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
- AlignmentI complement)
+ static protected AlignmentI openSplitFrame(AlignFrame thisFrame,
+ AlignFrame newAlignFrame, AlignmentI complement)
{
/*
* Make a new frame with a copy of the alignment we are adding to. If this
*/
AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+ copyMe.setTitle(thisFrame.getTitle());
+
AlignmentI al = newAlignFrame.viewport.getAlignment();
final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
{
FeatureColourI preferredColour = featureSettings
.getFeatureColour(type);
+ FeatureMatcherSetI preferredFilters = featureSettings
+ .getFeatureFilters(type);
+
FeatureColourI origColour = fr.getFeatureStyle(type);
if (!mergeOnly || (!origRenderOrder.contains(type)
|| origColour == null
{
fr.setColour(type, preferredColour);
}
+ if (preferredFilters != null
+ && (!mergeOnly || fr.getFeatureFilter(type) != null))
+ {
+ fr.setFeatureFilter(type, preferredFilters);
+ }
if (featureSettings.isFeatureDisplayed(type))
{
displayed.setVisible(type);
{
this.viewName = viewName;
}
+
}
*/
package jalview.gui;
- import jalview.analysis.AlignSeq;
- import jalview.analysis.AlignmentUtils;
- import jalview.datamodel.Alignment;
- import jalview.datamodel.AlignmentAnnotation;
- import jalview.datamodel.Annotation;
- import jalview.datamodel.HiddenColumns;
- import jalview.datamodel.Sequence;
- import jalview.datamodel.SequenceGroup;
- import jalview.datamodel.SequenceI;
- import jalview.io.FileFormat;
- import jalview.io.FormatAdapter;
- import jalview.util.Comparison;
- import jalview.util.MessageManager;
- import jalview.util.Platform;
- import jalview.workers.InformationThread;
-
import java.awt.Color;
import java.awt.Cursor;
import java.awt.Dimension;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
+ import jalview.analysis.AlignSeq;
+ import jalview.analysis.AlignmentUtils;
+ import jalview.datamodel.Alignment;
+ import jalview.datamodel.AlignmentAnnotation;
+ import jalview.datamodel.Annotation;
+ import jalview.datamodel.HiddenColumns;
+ import jalview.datamodel.Sequence;
+ import jalview.datamodel.SequenceGroup;
+ import jalview.datamodel.SequenceI;
+ import jalview.io.FileFormat;
+ import jalview.io.FormatAdapter;
+ import jalview.util.Comparison;
+ import jalview.util.MessageManager;
+ import jalview.util.Platform;
++import jalview.workers.InformationThread;
+
/**
* The panel that holds the labels for alignment annotations, providing
* tooltips, context menus, drag to reorder rows, and drag to adjust panel
pop.show(this, evt.getX(), evt.getY());
return;
}
+
+ final AlignmentAnnotation ann = aa[selectedRow];
+ final boolean isSequenceAnnotation = ann.sequenceRef != null;
+
item = new JMenuItem(EDITNAME);
item.addActionListener(this);
pop.add(item);
if (selectedRow < aa.length)
{
final String label = aa[selectedRow].label;
- if (!aa[selectedRow].autoCalculated)
+ if (!(aa[selectedRow].autoCalculated)
+ && !(InformationThread.HMM_CALC_ID.equals(ann.getCalcId())))
{
if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
{
pop.addSeparator();
// av and sequencegroup need to implement same interface for
item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
- aa[selectedRow].scaleColLabel);
+ aa[selectedRow].scaleColLabel);
item.addActionListener(this);
pop.add(item);
}
consclipbrd.addActionListener(this);
pop.add(consclipbrd);
}
+ else if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+ {
+ addHmmerMenu(pop, ann);
+ }
}
pop.show(this, evt.getX(), evt.getY());
}
/**
+ * Adds context menu options for (alignment or group) Hmmer annotation
+ *
+ * @param pop
+ * @param ann
+ */
+ protected void addHmmerMenu(JPopupMenu pop, final AlignmentAnnotation ann)
+ {
+ final boolean isGroupAnnotation = ann.groupRef != null;
+ pop.addSeparator();
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString(
+ "label.ignore_below_background_frequency"),
+ isGroupAnnotation
+ ? ann.groupRef
+ .isIgnoreBelowBackground()
+ : ap.av.isIgnoreBelowBackground());
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (isGroupAnnotation)
+ {
+ if (!ann.groupRef.isUseInfoLetterHeight())
+ {
+ ann.groupRef.setIgnoreBelowBackground(cbmi.getState());
+ // todo and recompute group annotation
+ }
+ }
+ else if (!ap.av.isInfoLetterHeight())
+ {
+ ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
+ // todo and recompute annotation
+ }
+ ap.alignmentChanged(); // todo not like this
+ }
+ });
+ pop.add(cbmi);
+ final JCheckBoxMenuItem letterHeight = new JCheckBoxMenuItem(
+ MessageManager.getString("label.use_info_for_height"),
+ isGroupAnnotation ? ann.groupRef.isUseInfoLetterHeight()
+ : ap.av.isInfoLetterHeight());
+ letterHeight.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (isGroupAnnotation)
+ {
+ ann.groupRef.setInfoLetterHeight((letterHeight.getState()));
+ ann.groupRef.setIgnoreBelowBackground(true);
+ // todo and recompute group annotation
+ }
+ else
+ {
+ ap.av.setInfoLetterHeight(letterHeight.getState(), ap);
+ ap.av.setIgnoreBelowBackground(true, ap);
+ // todo and recompute annotation
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(letterHeight);
+ if (isGroupAnnotation)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ ann.groupRef.isShowInformationHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setShowInformationHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ ann.groupRef.isShowHMMSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setShowHMMSequenceLogo(cprofl.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ ann.groupRef.isNormaliseHMMSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef
+ .setNormaliseHMMSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ ann.groupRef.setShowHMMSequenceLogo(true);
+ ap.repaint();
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowInformationHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowInformationHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ av.isShowHMMSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowHMMSequenceLogo(cprof.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseHMMSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowHMMSequenceLogo(true);
+ av.setNormaliseHMMSequenceLogo(cprofnorm.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofnorm);
+ }
+ }
+
+ /**
* A helper method that adds menu options for calculation and visualisation of
* group and/or alignment consensus annotation to a popup menu. This is
* designed to be reusable for either unwrapped mode (popup menu is shown on
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
ap.av.sendSelection();
}
-
}
}
return;
seqs, omitHidden, alignmentStartEnd);
Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(new StringSelection(output), Desktop.instance);
+ .setContents(new StringSelection(output), Desktop.getInstance());
HiddenColumns hiddenColumns = null;
av.getAlignment().getHiddenColumns());
}
- Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
- // of a consensus
- // sequence ? need to
- // flag
- // sequence as special.
+ // what is the dataset of a consensus sequence?
+ // need to flag sequence as special.
+ Desktop.getInstance().jalviewClipboard = new Object[] { seqs, ds,
hiddenColumns };
}
@Override
public void paintComponent(Graphics g)
{
-
int width = getWidth();
if (width == 0)
{
}
drawComponent(g2, true, width);
-
}
/**
import jalview.analysis.TreeBuilder;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.AlignViewportI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import javax.swing.event.InternalFrameEvent;
/**
- * A dialog where a user can choose and action Tree or PCA calculation options
+ * A dialog where a user can choose and action Tree or PCA calculation options.
+ *
+ * Allows also for dialog-free static methods openPCAPanel(...) and
+ * openTreePanel(...) for scripted use.
+ *
*/
+ @SuppressWarnings("serial")
public class CalculationChooser extends JPanel
{
/*
*/
private static boolean treeMatchGaps = true;
- private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
+ private static Font VERDANA_11PT;
private static final int MIN_TREE_SELECTION = 3;
private JCheckBox shorterSequence;
- final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
+ private static ComboBoxTooltipRenderer renderer; // BH was not static
List<String> tips = new ArrayList<>();
private PCAPanel pcaPanel;
/**
+ * Open a new Tree panel on the desktop statically. Params are standard (not
+ * set by Groovy). No dialog is opened.
+ *
+ * @param af
+ * @param treeType
+ * @param modelName
+ * @return null if successful; the string
+ * "label.you_need_at_least_n_sequences" if number of sequences
+ * selected is inappropriate
+ */
+ public static Object openTreePanel(AlignFrame af, String treeType,
+ String modelName)
+ {
+ return openTreePanel(af, treeType, modelName, null);
+ }
+
+ /**
+ * public static method for JalviewJS API to open a PCAPanel without
+ * necessarily using a dialog.
+ *
+ * @param af
+ * @param modelName
+ * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+ * if number of sequences selected is inappropriate
+ */
+ public static Object openPcaPanel(AlignFrame af, String modelName)
+ {
+ return openPcaPanel(af, modelName, null);
+ }
+
+ /**
* Constructor
*
* @param af
paramsPanel.add(includeGappedColumns);
paramsPanel.add(shorterSequence);
+ if (VERDANA_11PT == null)
+ {
+ VERDANA_11PT = new Font("Verdana", 0, 11);
+ }
/*
* OK / Cancel buttons
*/
title = title + " (" + af.getViewport().getViewName() + ")";
}
- Desktop.addInternalFrame(frame, title, width, height, false);
+ Desktop.addInternalFrame(frame, title, Desktop.FRAME_MAKE_VISIBLE, width, height, Desktop.FRAME_NOT_RESIZABLE, Desktop.FRAME_SET_MIN_SIZE_300);
calcChoicePanel.doLayout();
revalidate();
/*
*/
protected JComboBox<String> buildModelOptionsList()
{
- final JComboBox<String> scoreModelsCombo = new JComboBox<>();
+ JComboBox<String> scoreModelsCombo = new JComboBox<>();
+ if (renderer == null)
+ {
+ renderer = new ComboBoxTooltipRenderer();
+ }
scoreModelsCombo.setRenderer(renderer);
/*
* for backwards compatibility with Jalview < 2.8 (JAL-2962)
*/
if (nucleotide && forPca
- && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false))
+ && Cache.getDefault(Preferences.BLOSUM62_PCA_FOR_NUCLEOTIDE,
+ false))
{
filtered.add(scoreModels.getBlosum62());
}
*/
protected void openTreePanel(String modelName, SimilarityParamsI params)
{
+ Object ret = openTreePanel(af,
+ neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING
+ : TreeBuilder.AVERAGE_DISTANCE,
+ modelName, params);
+ if (ret instanceof String)
+ {
+ JvOptionPane.showMessageDialog(this, // was opening on Desktop?
+ MessageManager.formatMessage(
+ (String) ret,
+ MIN_TREE_SELECTION),
+ MessageManager.getString("label.not_enough_sequences"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ }
+ }
+
+ /**
+ * Open a new PCA panel on the desktop
+ *
+ * @param modelName
+ * @param params
+ */
+ protected void openPcaPanel(String modelName, SimilarityParamsI params)
+ {
+ Object ret = openPcaPanel(af, modelName, params);
+ if (ret instanceof String)
+ {
+ JvOptionPane.showInternalMessageDialog(this,
+ MessageManager.formatMessage(
+ (String) ret,
+ MIN_PCA_SELECTION),
+ MessageManager
+ .getString("label.sequence_selection_insufficient"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ // only used for test suite
+ pcaPanel = (PCAPanel) ret;
+ }
+
+ }
+
+ /**
+ * Open a new Tree panel on the desktop statically
+ *
+ * @param af
+ * @param treeType
+ * @param modelName
+ * @param params
+ * @return null, or the string "label.you_need_at_least_n_sequences" if number
+ * of sequences selected is inappropriate
+ */
+ public static Object openTreePanel(AlignFrame af, String treeType,
+ String modelName, SimilarityParamsI params)
+ {
+
/*
* gui validation shouldn't allow insufficient sequences here, but leave
* this check in in case this method gets exposed programmatically in future
*/
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
SequenceGroup sg = viewport.getSelectionGroup();
if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.you_need_at_least_n_sequences",
- MIN_TREE_SELECTION),
- MessageManager.getString("label.not_enough_sequences"),
- JvOptionPane.WARNING_MESSAGE);
- return;
+ return "label.you_need_at_least_n_sequences";
+ }
+
+ if (params == null)
+ {
+ params = getSimilarityParameters(false);
}
- String treeType = neighbourJoining.isSelected()
- ? TreeBuilder.NEIGHBOUR_JOINING
- : TreeBuilder.AVERAGE_DISTANCE;
af.newTreePanel(treeType, modelName, params);
+ return null;
}
/**
- * Open a new PCA panel on the desktop
+ * public static method for JalviewJS API
*
+ * @param af
* @param modelName
* @param params
+ * @return the PCAPanel, or null if number of sequences selected is
+ * inappropriate
*/
- protected void openPcaPanel(String modelName, SimilarityParamsI params)
+ public static Object openPcaPanel(AlignFrame af, String modelName,
+ SimilarityParamsI params)
{
-
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
/*
* gui validation shouldn't allow insufficient sequences here, but leave
* this check in in case this method gets exposed programmatically in future
+ *
+ *
*/
if (((viewport.getSelectionGroup() != null)
&& (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION)
&& (viewport.getSelectionGroup().getSize() > 0))
|| (viewport.getAlignment().getHeight() < MIN_PCA_SELECTION))
{
- JvOptionPane.showInternalMessageDialog(this,
- MessageManager.formatMessage(
- "label.you_need_at_least_n_sequences",
- MIN_PCA_SELECTION),
- MessageManager
- .getString("label.sequence_selection_insufficient"),
- JvOptionPane.WARNING_MESSAGE);
- return;
+ return "label.you_need_at_least_n_sequences";
+ }
+
+ if (params == null)
+ {
+ params = getSimilarityParameters(true);
}
/*
* construct the panel and kick off its calculation thread
*/
- pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
- new Thread(pcaPanel).start();
-
+ PCAPanel pcap = new PCAPanel(af.alignPanel, modelName, params);
+ new Thread(pcap).start();
+ return pcap;
}
/**
}
}
+
/**
* Returns a data bean holding parameters for similarity (or distance) model
* calculation
* @param doPCA
* @return
*/
- protected SimilarityParamsI getSimilarityParameters(boolean doPCA)
+ public static SimilarityParamsI getSimilarityParameters(
+ boolean doPCA)
{
// commented out: parameter choices read from gui widgets
// SimilarityParamsI params = new SimilarityParams(
return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
matchOnShortestLength);
+
}
/**
import java.util.List;
import java.util.ListIterator;
import java.util.Vector;
+import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.FutureTask;
import java.util.concurrent.Semaphore;
import javax.swing.AbstractAction;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+ import jalview.api.StructureSelectionManagerProvider;
+ import jalview.bin.ApplicationSingletonProvider;
+ import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.gui.ImageExporter.ImageWriterI;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+ import jalview.jbgui.GDesktop;
import jalview.jbgui.GSplitFrame;
import jalview.jbgui.GStructureViewer;
import jalview.project.Jalview2XML;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
- import jalview.util.ShortcutKeyMaskExWrapper;
import jalview.util.UrlConstants;
import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.WSDiscovererI;
import jalview.ws.params.ParamManager;
import jalview.ws.utils.UrlDownloadClient;
* @author $author$
* @version $Revision: 1.155 $
*/
- public class Desktop extends jalview.jbgui.GDesktop
+ @SuppressWarnings("serial")
+ public class Desktop extends GDesktop
implements DropTargetListener, ClipboardOwner, IProgressIndicator,
- jalview.api.StructureSelectionManagerProvider
+ StructureSelectionManagerProvider, ApplicationSingletonI
+
{
private static final String CITATION = "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+ "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
+ @SuppressWarnings("deprecation")
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
/**
* @param listener
* @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
*/
+ @Deprecated
public void addJalviewPropertyChangeListener(
PropertyChangeListener listener)
{
* @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
* java.beans.PropertyChangeListener)
*/
+ @Deprecated
public void addJalviewPropertyChangeListener(String propertyName,
PropertyChangeListener listener)
{
* @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
* java.beans.PropertyChangeListener)
*/
+ @Deprecated
public void removeJalviewPropertyChangeListener(String propertyName,
PropertyChangeListener listener)
{
listener);
}
- /** Singleton Desktop instance */
- public static Desktop instance;
+ private MyDesktopPane desktopPane;
- public static MyDesktopPane desktop;
+ public static MyDesktopPane getDesktopPane()
+ {
+ Desktop desktop = getInstance();
+ return desktop == null ? null : desktop.desktopPane;
+ }
- public static MyDesktopPane getDesktop()
+ /**
+ * Answers an 'application scope' singleton instance of this class. Separate
+ * SwingJS 'applets' running in the same browser page will each have a
+ * distinct instance of Desktop.
+ *
+ * @return
+ */
+ public static Desktop getInstance()
{
- // BH 2018 could use currentThread() here as a reference to a
- // Hashtable<Thread, MyDesktopPane> in JavaScript
- return desktop;
+ return Jalview.isHeadlessMode() ? null
+ : (Desktop) ApplicationSingletonProvider
+ .getInstance(Desktop.class);
}
- static int openFrameCount = 0;
+ public static StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager
+ .getStructureSelectionManager(getInstance());
+ }
+
+ int openFrameCount = 0;
- static final int xOffset = 30;
+ final int xOffset = 30;
- static final int yOffset = 30;
+ final int yOffset = 30;
- public static jalview.ws.jws1.Discoverer discoverer;
+ public jalview.ws.jws1.Discoverer discoverer;
- public static Object[] jalviewClipboard;
+ public Object[] jalviewClipboard;
- public static boolean internalCopy = false;
+ public boolean internalCopy = false;
- static int fileLoadingCount = 0;
+ int fileLoadingCount = 0;
class MyDesktopManager implements DesktopManager
{
} catch (NullPointerException npe)
{
Point p = getMousePosition();
- instance.showPasteMenu(p.x, p.y);
+ showPasteMenu(p.x, p.y);
}
}
public void endDraggingFrame(JComponent f)
{
delegate.endDraggingFrame(f);
- desktop.repaint();
+ desktopPane.repaint();
}
@Override
public void endResizingFrame(JComponent f)
{
delegate.endResizingFrame(f);
- desktop.repaint();
+ desktopPane.repaint();
}
@Override
}
/**
- * Creates a new Desktop object.
+ * Private constructor enforces singleton pattern. It is called by reflection
+ * from ApplicationSingletonProvider.getInstance().
*/
- public Desktop()
+ private Desktop()
{
- super();
- /**
- * A note to implementors. It is ESSENTIAL that any activities that might
- * block are spawned off as threads rather than waited for during this
- * constructor.
- */
- instance = this;
-
- doConfigureStructurePrefs();
- setTitle("Jalview " + Cache.getProperty("VERSION"));
- /*
- if (!Platform.isAMac())
- {
- // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
- }
- else
- {
- this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
- }
- */
-
+ Cache.initLogger();
try
{
- APQHandlers.setAPQHandlers(this);
- } catch (Throwable t)
- {
- System.out.println("Error setting APQHandlers: " + t.toString());
- // t.printStackTrace();
- }
-
- addWindowListener(new WindowAdapter()
- {
+ /**
+ * A note to implementors. It is ESSENTIAL that any activities that might
+ * block are spawned off as threads rather than waited for during this
+ * constructor.
+ */
- @Override
- public void windowClosing(WindowEvent ev)
+ doConfigureStructurePrefs();
+ setTitle("Jalview " + Cache.getProperty("VERSION"));
+ /*
+ if (!Platform.isAMac())
{
- quit();
+ // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
}
- });
+ else
+ {
+ this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+ }
+ */
- boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE",
- false);
+ try
+ {
+ APQHandlers.setAPQHandlers(this);
+ } catch (Throwable t)
+ {
+ System.out.println("Error setting APQHandlers: " + t.toString());
+ // t.printStackTrace();
+ }
- boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE",
- false);
- desktop = new MyDesktopPane(selmemusage);
+ addWindowListener(new WindowAdapter()
+ {
- showMemusage.setSelected(selmemusage);
- desktop.setBackground(Color.white);
+ @Override
+ public void windowClosing(WindowEvent ev)
+ {
+ quit();
+ }
+ });
- getContentPane().setLayout(new BorderLayout());
- // alternate config - have scrollbars - see notes in JAL-153
- // JScrollPane sp = new JScrollPane();
- // sp.getViewport().setView(desktop);
- // getContentPane().add(sp, BorderLayout.CENTER);
+ boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false);
- // BH 2018 - just an experiment to try unclipped JInternalFrames.
- if (Platform.isJS())
- {
- getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
- }
+ boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE", false);
+ desktopPane = new MyDesktopPane(selmemusage);
- getContentPane().add(desktop, BorderLayout.CENTER);
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+ showMemusage.setSelected(selmemusage);
+ desktopPane.setBackground(Color.white);
- // This line prevents Windows Look&Feel resizing all new windows to maximum
- // if previous window was maximised
- desktop.setDesktopManager(new MyDesktopManager(
- (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
- : Platform.isAMacAndNotJS()
- ? new AquaInternalFrameManager(
- desktop.getDesktopManager())
- : desktop.getDesktopManager())));
+ getContentPane().setLayout(new BorderLayout());
+ // alternate config - have scrollbars - see notes in JAL-153
+ // JScrollPane sp = new JScrollPane();
+ // sp.getViewport().setView(desktop);
+ // getContentPane().add(sp, BorderLayout.CENTER);
- Rectangle dims = getLastKnownDimensions("");
- if (dims != null)
- {
- setBounds(dims);
- }
- else
- {
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- int xPos = Math.max(5, (screenSize.width - 900) / 2);
- int yPos = Math.max(5, (screenSize.height - 650) / 2);
- setBounds(xPos, yPos, 900, 650);
- }
+ // BH 2018 - just an experiment to try unclipped JInternalFrames.
+ if (Platform.isJS())
+ {
+ getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
+ }
- if (!Platform.isJS())
- /**
- * Java only
- *
- * @j2sIgnore
- */
- {
- jconsole = new Console(this, showjconsole);
- jconsole.setHeader(Cache.getVersionDetailsForConsole());
- showConsole(showjconsole);
+ getContentPane().add(desktopPane, BorderLayout.CENTER);
+ desktopPane.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
- showNews.setVisible(false);
+ // This line prevents Windows Look&Feel resizing all new windows to
+ // maximum
+ // if previous window was maximised
+ desktopPane.setDesktopManager(new MyDesktopManager(
+ (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+ : Platform.isAMacAndNotJS()
+ ? new AquaInternalFrameManager(
+ desktopPane.getDesktopManager())
+ : desktopPane.getDesktopManager())));
- experimentalFeatures.setSelected(showExperimental());
+ Rectangle dims = getLastKnownDimensions("");
+ if (dims != null)
+ {
+ setBounds(dims);
+ }
+ else
+ {
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+ int xPos = Math.max(5, (screenSize.width - 900) / 2);
+ int yPos = Math.max(5, (screenSize.height - 650) / 2);
+ setBounds(xPos, yPos, 900, 650);
+ }
getIdentifiersOrgData();
- checkURLLinks();
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ jconsole = new Console(this, showjconsole);
+ jconsole.setHeader(Cache.getVersionDetailsForConsole());
+ showConsole(showjconsole);
- // Spawn a thread that shows the splashscreen
+ showNews.setVisible(false);
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- new SplashScreen(true);
- }
- });
+ experimentalFeatures.setSelected(showExperimental());
- // Thread off a new instance of the file chooser - this reduces the time
- // it
- // takes to open it later on.
- new Thread(new Runnable()
- {
- @Override
- public void run()
+ if (Jalview.isInteractive())
{
- Cache.log.debug("Filechooser init thread started.");
- String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
- fileFormat);
- Cache.log.debug("Filechooser init thread finished.");
- }
- }).start();
- // Add the service change listener
- changeSupport.addJalviewPropertyChangeListener("services",
- new PropertyChangeListener()
- {
+ // disabled for SeqCanvasTest
+ checkURLLinks();
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- Cache.log.debug("Firing service changed event for "
- + evt.getNewValue());
- JalviewServicesChanged(evt);
- }
- });
- }
+ // Spawn a thread that shows the splashscreen
- this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ new SplashScreen(true);
+ }
+ });
- this.addWindowListener(new WindowAdapter()
- {
- @Override
- public void windowClosing(WindowEvent evt)
- {
- quit();
+ // Thread off a new instance of the file chooser - this reduces the
+ // time
+ // it
+ // takes to open it later on.
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Filechooser init thread started.");
+ String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ JalviewFileChooser.forRead(
+ Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ Cache.log.debug("Filechooser init thread finished.");
+ }
+ }).start();
+ // Add the service change listener
+ changeSupport.addJalviewPropertyChangeListener("services",
+ new PropertyChangeListener()
+ {
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ Cache.log.debug("Firing service changed event for "
+ + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
+ });
+ }
}
- });
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this));
- MouseAdapter ma;
- this.addMouseListener(ma = new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
+ this.addWindowListener(new WindowAdapter()
{
- if (evt.isPopupTrigger()) // Mac
+ @Override
+ public void windowClosing(WindowEvent evt)
{
- showPasteMenu(evt.getX(), evt.getY());
+ quit();
}
- }
+ });
- @Override
- public void mouseReleased(MouseEvent evt)
+ MouseAdapter ma;
+ this.addMouseListener(ma = new MouseAdapter()
{
- if (evt.isPopupTrigger()) // Windows
+ @Override
+ public void mousePressed(MouseEvent evt)
{
- showPasteMenu(evt.getX(), evt.getY());
+ if (evt.isPopupTrigger()) // Mac
+ {
+ showPasteMenu(evt.getX(), evt.getY());
+ }
}
- }
- });
- desktop.addMouseListener(ma);
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
+ {
+ showPasteMenu(evt.getX(), evt.getY());
+ }
+ }
+ });
+ desktopPane.addMouseListener(ma);
+ } catch (Throwable t)
+ {
+ t.printStackTrace();
+ }
}
.getStructureSelectionManager(this);
if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
{
- ssm.setAddTempFacAnnot(Cache
- .getDefault(Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(Cache
- .getDefault(Preferences.STRUCT_FROM_PDB, true));
+ ssm.setAddTempFacAnnot(
+ Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+ ssm.setProcessSecondaryStructure(
+ Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
ssm.setSecStructServices(
Cache.getDefault(Preferences.USE_RNAVIEW, true));
}
}
}
}).start();
-
+
}
@Override
public void run()
{
long now = System.currentTimeMillis();
- Desktop.instance.setProgressBar(
- MessageManager.getString("status.refreshing_news"), now);
+ setProgressBar(MessageManager.getString("status.refreshing_news"),
+ now);
jvnews.refreshNews();
- Desktop.instance.setProgressBar(null, now);
+ setProgressBar(null, now);
jvnews.showNews();
}
}).start();
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
String x = Cache.getProperty(windowName + "SCREEN_X");
String y = Cache.getProperty(windowName + "SCREEN_Y");
- String width = Cache
- .getProperty(windowName + "SCREEN_WIDTH");
- String height = Cache
- .getProperty(windowName + "SCREEN_HEIGHT");
+ String width = Cache.getProperty(windowName + "SCREEN_WIDTH");
+ String height = Cache.getProperty(windowName + "SCREEN_HEIGHT");
if ((x != null) && (y != null) && (width != null) && (height != null))
{
int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
// attempt #1 - try to cope with change in screen geometry - this
// version doesn't preserve original jv aspect ratio.
// take ratio of current screen size vs original screen size.
- double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(
- Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
- double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(
- Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
+ double sw = ((1f * screenSize.width) / (1f * Integer
+ .parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
+ double sh = ((1f * screenSize.height) / (1f * Integer
+ .parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
// rescale the bounds depending upon the current screen geometry.
ix = (int) (ix * sw);
iw = (int) (iw * sw);
}
}
- /**
- * Adds and opens the given frame to the desktop
- *
- * @param frame
- * Frame to show
- * @param title
- * Visible Title
- * @param w
- * width
- * @param h
- * height
- */
- public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, int w, int h)
- {
- addInternalFrame(frame, title, true, w, h, true, false);
- }
-
- /**
- * Add an internal frame to the Jalview desktop
- *
- * @param frame
- * Frame to show
- * @param title
- * Visible Title
- * @param makeVisible
- * When true, display frame immediately, otherwise, caller must call
- * setVisible themselves.
- * @param w
- * width
- * @param h
- * height
- */
- public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, boolean makeVisible,
- int w, int h)
- {
- addInternalFrame(frame, title, makeVisible, w, h, true, false);
- }
+ // /**
+ // * Add an internal frame to the Jalview desktop that is allowed to be resized,
+ // * has a minimum size of 300px and might or might not be visible
+ // *
+ // * @param frame
+ // * Frame to show
+ // * @param title
+ // * Visible Title
+ // * @param makeVisible
+ // * When true, display frame immediately, otherwise, caller must call
+ // * setVisible themselves.
+ // * @param w
+ // * width
+ // * @param h
+ // * height
+ // */
+ // @Deprecated
+ // public static synchronized void addInternalFrame(
+ // final JInternalFrame frame, String title, boolean makeVisible,
+ // int w, int h)
+ // {
+ // // textbox, web services, sequenceFetcher, featureSettings
+ // getInstance().addFrame(frame, title, makeVisible, w, h,
+ // FRAME_ALLOW_RESIZE, FRAME_SET_MIN_SIZE_300);
+ // }
+ //
+ // /**
+ // * Add an internal frame to the Jalview desktop that is visible, has a minimum
+ // * size of 300px, and may or may not be resizable
+ // *
+ // * @param frame
+ // * Frame to show
+ // * @param title
+ // * Visible Title
+ // * @param w
+ // * width
+ // * @param h
+ // * height
+ // * @param resizable
+ // * Allow resize
+ // */
+ // @Deprecated
+ // public static synchronized void addInternalFrame(
+ // final JInternalFrame frame, String title, int w, int h,
+ // boolean resizable)
+ // {
+ // // annotation, font, calculation, user-defined colors
+ // getInstance().addFrame(frame, title, FRAME_MAKE_VISIBLE, w, h,
+ // resizable, FRAME_SET_MIN_SIZE_300);
+ // }
/**
- * Add an internal frame to the Jalview desktop and make it visible
+ * Adds and opens the given frame to the desktop that is visible, allowed to
+ * resize, and has a 300px minimum width.
*
* @param frame
* Frame to show
* width
* @param h
* height
- * @param resizable
- * Allow resize
*/
public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, int w, int h,
- boolean resizable)
+ final JInternalFrame frame, String title, int w, int h)
{
- addInternalFrame(frame, title, true, w, h, resizable, false);
+ // 58 classes
+
+ addInternalFrame(frame, title, Desktop.FRAME_MAKE_VISIBLE, w, h,
+ FRAME_ALLOW_RESIZE, FRAME_SET_MIN_SIZE_300);
}
/**
- * Add an internal frame to the Jalview desktop
+ * Add an internal frame to the Jalview desktop that may optionally be
+ * visible, resizable, and allowed to be any size
*
* @param frame
* Frame to show
final JInternalFrame frame, String title, boolean makeVisible,
int w, int h, boolean resizable, boolean ignoreMinSize)
{
-
+ // 15 classes call this method directly.
+
// TODO: allow callers to determine X and Y position of frame (eg. via
// bounds object).
// TODO: consider fixing method to update entries in the window submenu with
{
frame.setSize(w, h);
}
- // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
- // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
- // IF JALVIEW IS RUNNING HEADLESS
- // ///////////////////////////////////////////////
- if (instance == null || (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true")))
- {
- return;
- }
+ if (getInstance() != null)
+ getInstance().addFrame(frame, makeVisible, resizable,
+ ignoreMinSize);
+ }
- openFrameCount++;
+ // These can now by put into a single int flag, if desired:
+
+ public final static boolean FRAME_MAKE_VISIBLE = true;
+
+ public final static boolean FRAME_NOT_VISIBLE = false;
+
+ public final static boolean FRAME_ALLOW_RESIZE = true;
+
+ public final static boolean FRAME_NOT_RESIZABLE = false;
+
+ public final static boolean FRAME_ALLOW_ANY_SIZE = true;
+ public final static boolean FRAME_SET_MIN_SIZE_300 = false;
+
+ private void addFrame(JInternalFrame frame,
+ boolean makeVisible, boolean resizable,
+ boolean ignoreMinSize)
+ {
+
+ openFrameCount++;
+
+ boolean isEmbedded = (Platform.getEmbeddedAttribute(frame, "id") != null);
+ boolean hasEmbeddedSize = (Platform.getDimIfEmbedded(frame, -1, -1) != null);
+ // Web page embedding allows us to ignore minimum size
+ ignoreMinSize |= hasEmbeddedSize;
+
if (!ignoreMinSize)
{
- frame.setMinimumSize(
- new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
-
// Set default dimension for Alignment Frame window.
// The Alignment Frame window could be added from a number of places,
// hence,
{
frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH,
ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
+ } else {
+ frame.setMinimumSize(
+ new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
+
}
}
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
frame.setOpaque(Platform.isJS());
-
- if (frame.getX() < 1 && frame.getY() < 1)
+ if (!isEmbedded && frame.getX() < 1 && frame.getY() < 1)
{
frame.setLocation(xOffset * openFrameCount,
yOffset * ((openFrameCount - 1) % 10) + yOffset);
* add an entry for the new frame in the Window menu
* (and remove it when the frame is closed)
*/
- final JMenuItem menuItem = new JMenuItem(title);
+ final JMenuItem menuItem = new JMenuItem(frame.getTitle());
frame.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
public void internalFrameActivated(InternalFrameEvent evt)
{
- JInternalFrame itf = desktop.getSelectedFrame();
+ JInternalFrame itf = getDesktopPane().getSelectedFrame();
if (itf != null)
{
if (itf instanceof AlignFrame)
{
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
- windowMenu.remove(menuItem);
+ getInstance().windowMenu.remove(menuItem);
}
});
setKeyBindings(frame);
- desktop.add(frame);
+ getDesktopPane().add(frame);
- windowMenu.add(menuItem);
+ getInstance().windowMenu.add(menuItem);
frame.toFront();
try
}
/**
- * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the
- * window
+ * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
+ * the window
*
* @param frame
*/
private static void setKeyBindings(JInternalFrame frame)
{
- @SuppressWarnings("serial")
final Action closeAction = new AbstractAction()
{
@Override
KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
InputEvent.CTRL_DOWN_MASK);
KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
+ Platform.SHORTCUT_KEY_MASK);
InputMap inputMap = frame
.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
{
if (!internalCopy)
{
- Desktop.jalviewClipboard = null;
+ jalviewClipboard = null;
}
internalCopy = false;
try
{
- Desktop.transferFromDropTarget(files, protocols, evt, t);
+ transferFromDropTarget(files, protocols, evt, t);
} catch (Exception e)
{
e.printStackTrace();
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser chooser = JalviewFileChooser
- .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled());
+ JalviewFileChooser chooser = JalviewFileChooser.forRead(
+ Cache.getProperty("LAST_DIRECTORY"), fileFormat,
+ BackupFiles.getEnabled());
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
{
String msg = MessageManager
.formatMessage("label.couldnt_locate", url);
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+ JvOptionPane.showInternalMessageDialog(getDesktopPane(), msg,
MessageManager.getString("label.url_not_found"),
JvOptionPane.WARNING_MESSAGE);
};
String dialogOption = MessageManager
.getString("label.input_alignment_from_url");
- JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action)
+ JvOptionPane.newOptionDialog(desktopPane).setResponseHandler(0, action)
.showInternalDialog(panel, dialogOption,
JvOptionPane.YES_NO_CANCEL_OPTION,
JvOptionPane.PLAIN_MESSAGE, null, options,
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(viewPanel);
- Desktop.addInternalFrame(cap,
- MessageManager.getString("label.cut_paste_alignmen_file"), true,
- 600, 500);
+ addInternalFrame(cap,
+ MessageManager.getString("label.cut_paste_alignmen_file"),
+ FRAME_MAKE_VISIBLE, 600, 500, FRAME_ALLOW_RESIZE,
+ FRAME_SET_MIN_SIZE_300);
}
/*
public void quit()
{
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- Cache.setProperty("SCREENGEOMETRY_WIDTH",
- screen.width + "");
- Cache.setProperty("SCREENGEOMETRY_HEIGHT",
- screen.height + "");
+ Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+ Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
getWidth(), getHeight()));
private void storeLastKnownDimensions(String string, Rectangle jc)
{
- Cache.log.debug("Storing last known dimensions for "
- + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
- + " height:" + jc.height);
+ Cache.log.debug("Storing last known dimensions for " + string + ": x:"
+ + jc.x + " y:" + jc.y + " width:" + jc.width + " height:"
+ + jc.height);
Cache.setProperty(string + "SCREEN_X", jc.x + "");
Cache.setProperty(string + "SCREEN_Y", jc.y + "");
public void closeAll_actionPerformed(ActionEvent e)
{
// TODO show a progress bar while closing?
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
for (int i = 0; i < frames.length; i++)
{
try
@Override
protected void showMemusage_actionPerformed(ActionEvent e)
{
- desktop.showMemoryUsage(showMemusage.isSelected());
+ desktopPane.showMemoryUsage(showMemusage.isSelected());
}
/*
void reorderAssociatedWindows(boolean minimize, boolean close)
{
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
if (frames == null || frames.length < 1)
{
return;
}
- AlignmentViewport source = null, target = null;
+ AlignViewportI source = null;
+ AlignViewportI target = null;
if (frames[0] instanceof AlignFrame)
{
source = ((AlignFrame) frames[0]).getCurrentView();
setProgressBar(MessageManager.formatMessage(
"label.saving_jalview_project", new Object[]
{ chosenFile.getName() }), chosenFile.hashCode());
- Cache.setProperty("LAST_DIRECTORY",
- chosenFile.getParent());
+ Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
try
{
- boolean doBackup = BackupFiles.getEnabled();
- BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null;
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile)
+ : null;
- new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile);
+ new Jalview2XML().saveState(
+ doBackup ? backupfiles.getTempFile() : chosenFile);
if (doBackup)
{
setProgressBar(null, chosenFile.hashCode());
}
}).start();
- }
+ }
}
@Override
"Jalview Project (old)" };
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
- "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles,
- // allowBackupFiles
+ "Jalview Project", true, BackupFiles.getEnabled()); // last two
+ // booleans:
+ // allFiles,
+ // allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
chooser.setResponseHandler(0, new Runnable()
@Override
public void run()
{
- try
+ try
{
new Jalview2XML().loadJalviewAlign(selectedFile);
} catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
- {
- Cache.log.error(
- "Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.error_whilst_loading_project_from",
- new Object[]
- { choice }),
- MessageManager.getString("label.couldnt_load_project"),
- JvOptionPane.WARNING_MESSAGE);
- }
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(getDesktopPane(),
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager
+ .getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
}
}).start();
}
});
-
+
chooser.showOpenDialog(this);
}
{
progressPanel = new JPanel(new GridLayout(1, 1));
totalProgressCount = 0;
- instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+ getContentPane().add(progressPanel, BorderLayout.SOUTH);
}
JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
JProgressBar progressBar = new JProgressBar();
((GridLayout) progressPanel.getLayout()).setRows(
((GridLayout) progressPanel.getLayout()).getRows() + 1);
++totalProgressCount;
- instance.validate();
+ validate();
return thisprogress;
}
*/
public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
{
- if (Desktop.desktop == null)
+ if (getDesktopPane() == null)
{
// no frames created and in headless mode
// TODO: verify that frames are recoverable when in headless mode
public static AlignmentViewport[] getViewports(String sequenceSetId)
{
List<AlignmentViewport> viewp = new ArrayList<>();
- if (desktop != null)
+ if (getDesktopPane() != null)
{
- AlignFrame[] frames = Desktop.getAlignFrames();
+ AlignFrame[] frames = getAlignFrames();
for (AlignFrame afr : frames)
{
// FIXME: ideally should use UI interface API
FeatureSettings viewFeatureSettings = (af.featureSettings != null
- && af.featureSettings.isOpen())
- ? af.featureSettings
- : null;
+ && af.featureSettings.isOpen()) ? af.featureSettings : null;
Rectangle fsBounds = af.getFeatureSettingsGeometry();
for (int i = 0; i < size; i++)
{
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- // and materialise a new feature settings dialog instance for the new alignframe
+ // and materialise a new feature settings dialog instance for the new
+ // alignframe
// (closes the old as if 'OK' was pressed)
if (ap == af.alignPanel && newaf.featureSettings != null
&& newaf.featureSettings.isOpen()
/**
* Gather expanded views (separate AlignFrame's) with the same sequence set
- * identifier back in to this frame as additional views, and close the expanded
- * views. Note the expanded frames may themselves have multiple views. We take
- * the lot.
+ * identifier back in to this frame as additional views, and close the
+ * expanded views. Note the expanded frames may themselves have multiple
+ * views. We take the lot.
*
* @param source
*/
{
source.viewport.setGatherViewsHere(true);
source.viewport.setExplodedGeometry(source.getBounds());
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
String viewId = source.viewport.getSequenceSetId();
for (int t = 0; t < frames.length; t++)
{
}
// refresh the feature setting UI for the source frame if it exists
- if (source.featureSettings != null
- && source.featureSettings.isOpen())
+ if (source.featureSettings != null && source.featureSettings.isOpen())
{
source.showFeatureSettingsUI();
}
public JInternalFrame[] getAllFrames()
{
- return desktop.getAllFrames();
+ return desktopPane.getAllFrames();
}
/**
});
msgPanel.add(jcb);
- JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
+ JvOptionPane.showMessageDialog(desktopPane, msgPanel,
MessageManager
.getString("label.SEQUENCE_ID_no_longer_used"),
JvOptionPane.WARNING_MESSAGE);
/**
* Proxy class for JDesktopPane which optionally displays the current memory
- * usage and highlights the desktop area with a red bar if free memory runs low.
+ * usage and highlights the desktop area with a red bar if free memory runs
+ * low.
*
* @author AMW
*/
- public class MyDesktopPane extends JDesktopPane
- implements Runnable
+ public class MyDesktopPane extends JDesktopPane implements Runnable
{
private static final float ONE_MB = 1048576f;
{
if (Jalview.isHeadlessMode())
{
- // Desktop.desktop is null in headless mode
- return new AlignFrame[] { Jalview.currentAlignFrame };
+ return new AlignFrame[] { Jalview.getInstance().currentAlignFrame };
}
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = getDesktopPane().getAllFrames();
if (frames == null)
{
*/
public GStructureViewer[] getJmols()
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
if (frames == null)
{
} catch (Exception ex)
{
Cache.log.error("Groovy Shell Creation failed.", ex);
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(desktopPane,
MessageManager.getString("label.couldnt_create_groovy_shell"),
MessageManager.getString("label.groovy_support_failed"),
}
/**
- * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding
- * when opened
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
+ * binding when opened
*/
protected void addQuitHandler()
{
+
getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
.put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
+ Platform.SHORTCUT_KEY_MASK),
"Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
progressBars.put(Long.valueOf(id), addProgressPanel(message));
}
}
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ //TODO
+ throw new UnsupportedOperationException("not implemented");
+ }
/*
* (non-Javadoc)
}
/**
- * This will return the first AlignFrame holding the given viewport instance. It
- * will break if there are more than one AlignFrames viewing a particular av.
+ * This will return the first AlignFrame holding the given viewport instance.
+ * It will break if there are more than one AlignFrames viewing a particular
+ * av.
*
* @param viewport
* @return alignFrame for viewport
*/
public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
{
- if (desktop != null)
+ if (getDesktopPane() != null)
{
AlignmentPanel[] aps = getAlignmentPanels(
viewport.getSequenceSetId());
public void startServiceDiscovery(boolean blocking)
{
- boolean alive = true;
- Thread t0 = null, t1 = null, t2 = null;
+ System.out.println("Starting service discovery");
+ var tasks = new ArrayList<Future<?>>();
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
- if (true)
+
+ System.out.println("loading services");
+
+ /** @j2sIgnore */
{
// todo: changesupport handlers need to be transferred
if (discoverer == null)
{
- discoverer = new jalview.ws.jws1.Discoverer();
+ discoverer = jalview.ws.jws1.Discoverer.getInstance();
// register PCS handler for desktop.
discoverer.addPropertyChangeListener(changeSupport);
}
// JAL-940 - disabled JWS1 service configuration - always start discoverer
// until we phase out completely
- (t0 = new Thread(discoverer)).start();
+ var f = new FutureTask<Void>(discoverer, null);
+ new Thread(f).start();
+ tasks.add(f);
}
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- tasks.add(jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer());
- t2 = jalview.ws.jws2.Jws2Discoverer.getInstance()
- .startDiscoverer(changeSupport);
++ tasks.add(jalview.ws.jws2.Jws2Discoverer.getInstance().startDiscoverer());
}
- Thread t3 = null;
+ if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
- // TODO: do rest service discovery
+ tasks.add(jalview.ws.slivkaws.SlivkaWSDiscoverer.getInstance().startDiscoverer());
}
if (blocking)
{
- while (alive)
- {
+ for (Future<?> task : tasks) {
try
{
- Thread.sleep(15);
+ // block until all discovery tasks are done
+ task.get();
} catch (Exception e)
{
+ e.printStackTrace();
}
- alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
- || (t3 != null && t3.isAlive())
- || (t0 != null && t0.isAlive());
}
}
}
{
if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
{
- final String ermsg = jalview.ws.jws2.Jws2Discoverer.getInstance()
- .getErrorMessages();
+ final WSDiscovererI discoverer = jalview.ws.jws2.Jws2Discoverer
- .getDiscoverer();
++ .getInstance();
+ final String ermsg = discoverer.getErrorMessages();
++ // CONFLICT:ALT:? final String ermsg = jalview.ws.jws2.Jws2Discoverer.getInstance()
if (ermsg != null)
{
if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
*
* jd.waitForInput();
*/
- JvOptionPane.showConfirmDialog(Desktop.desktop,
+ JvOptionPane.showConfirmDialog(desktopPane,
new JLabel("<html><table width=\"450\"><tr><td>"
+ ermsg + "</td></tr></table>"
+ "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
*/
public static void showUrl(final String url)
{
- showUrl(url, Desktop.instance);
+ showUrl(url, getInstance());
}
/**
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(getDesktopPane(),
MessageManager
.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
try
{
url = e.getURL().toString();
- Desktop.showUrl(url);
+ showUrl(url);
} catch (Exception x)
{
if (url != null)
{
}
}
- if (instance == null)
+ if (Jalview.isHeadlessMode())
{
return;
}
/**
* Explode the views in the given SplitFrame into separate SplitFrame windows.
- * This respects (remembers) any previous 'exploded geometry' i.e. the size and
- * location last time the view was expanded (if any). However it does not
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size
+ * and location last time the view was expanded (if any). However it does not
* remember the split pane divider location - this is set to match the
* 'exploding' frame.
*
{
splitFrame.setLocation(geometry.getLocation());
}
- Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
+ addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
}
/*
String topViewId = myTopFrame.viewport.getSequenceSetId();
String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof SplitFrame && frame != source)
* - the payload from the drop event
* @throws Exception
*/
+ @SuppressWarnings("unchecked")
public static void transferFromDropTarget(List<Object> files,
List<DataSourceType> protocols, DropTargetDropEvent evt,
Transferable t) throws Exception
{
- // BH 2018 changed List<String> to List<Object> to allow for File from SwingJS
+ // BH 2018 changed List<String> to List<Object> to allow for File from
+ // SwingJS
// DataFlavor[] flavors = t.getTransferDataFlavors();
// for (int i = 0; i < flavors.length; i++) {
// byte[] data = getDroppedFileBytes(file);
// fileName.setText(file.getName() + " - " + data.length + " " +
// evt.getLocation());
- // JTextArea target = (JTextArea) ((DropTarget) evt.getSource()).getComponent();
+ // JTextArea target = (JTextArea) ((DropTarget)
+ // evt.getSource()).getComponent();
// target.setText(new String(data));
// }
// dtde.dropComplete(true);
{
// Works on Windows and MacOSX
Cache.log.debug("Drop handled as javaFileListFlavor");
- for (Object file : (List) t
+ for (File file : (List<File>) t
.getTransferData(DataFlavor.javaFileListFlavor))
{
files.add(file);
}
/**
- * Answers a (possibly empty) list of any structure viewer frames (currently for
- * either Jmol or Chimera) which are currently open. This may optionally be
- * restricted to viewers of a specified class, or viewers linked to a specified
- * alignment panel.
+ * Answers a (possibly empty) list of any structure viewer frames (currently
+ * for either Jmol or Chimera) which are currently open. This may optionally
+ * be restricted to viewers of a specified class, or viewers linked to a
+ * specified alignment panel.
*
* @param apanel
* if not null, only return viewers linked to this panel
Class<? extends StructureViewerBase> structureViewerClass)
{
List<StructureViewerBase> result = new ArrayList<>();
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ JInternalFrame[] frames = getAllFrames();
for (JInternalFrame frame : frames)
{
}
return result;
}
+
}
*/
package jalview.gui;
- import jalview.util.MessageManager;
-
-import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
+import java.awt.Container;
import java.awt.Font;
-import java.awt.GridLayout;
-import java.awt.Rectangle;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JComponent;
-import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JPanel;
import javax.swing.JScrollBar;
import javax.swing.SwingConstants;
import javax.swing.border.Border;
import javax.swing.border.TitledBorder;
+ import jalview.util.MessageManager;
+ import jalview.util.Platform;
+
/**
* useful functions for building Swing GUIs
*
*/
public final class JvSwingUtils
{
+ static final String HTML_PREFIX = (Platform.isJS() ?
+ "<html><div style=\"max-width:350px;overflow-wrap:break-word;display:inline-block\">"
+ : "<html><div style=\"width:350; text-align: justify; word-wrap: break-word;\">"
+ );
+
/**
* wrap a bare html safe string to around 60 characters per line using a CSS
* style class specifying word-wrap and break-word
*
* @param enclose
- * if true, add <html> wrapper tags
+ * if true, add <html> wrapper tags (currently false for only
+ * two references -- both in Jws2Discoverer --
* @param ttext
*
* @return
{
Objects.requireNonNull(ttext,
"Tootip text to format must not be null!");
- ttext = ttext.trim();
- boolean maxLengthExceeded = false;
+ ttext = ttext.trim().replaceAll("<br/>", "<br>");
- if (ttext.contains("<br>"))
+ boolean maxLengthExceeded = false;
+ boolean isHTML = ttext.startsWith("<html>");
+ if (isHTML)
{
- String[] htmllines = ttext.split("<br>");
- for (String line : htmllines)
- {
- maxLengthExceeded = line.length() > 60;
- if (maxLengthExceeded)
- {
+ ttext = ttext.substring(6);
+ }
+ if (ttext.endsWith("</html>"))
+ {
+ isHTML = true;
+ ttext = ttext.substring(0, ttext.length() - 7);
+ }
+ boolean hasBR = ttext.contains("<br>");
+ enclose |= isHTML || hasBR;
+ if (hasBR)
+ {
+ int pt = -1, ptlast = -4;
+ while ((pt = ttext.indexOf("<br>", pt + 1)) >= 0) {
+ if (pt - ptlast - 4 > 60) {
+ maxLengthExceeded = true;
break;
}
}
}
- else
+ else
{
maxLengthExceeded = ttext.length() > 60;
}
- if (!maxLengthExceeded)
- {
- return enclose ? "<html>" + ttext + "</html>" : ttext;
- }
-
- return (enclose ? "<html>" : "")
- // BH 2018
- + "<style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style><div class=\"ttip\">"
- // + "<style> p.ttip {width:350px;margin:-14px 0px -14px 0px;padding:2px;overflow-wrap:break-word;}"
- // + "</style><p class=\"ttip\">"
- + ttext
- + " </div>"
- // + "</p>"
- + ((enclose ? "</html>" : ""));
+ String ret = (!enclose ? ttext : maxLengthExceeded ? HTML_PREFIX + ttext + "</div></html>" :
+ "<html>" + ttext + "</html>");
+ //System.out.println("JvSwUtil " + enclose + " " + maxLengthExceeded + " " + ret);
+ return ret;
}
public static JButton makeButton(String label, String tooltip,
}
/**
+ * A convenience method that that adds a component with label to a container,
+ * sets a tooltip on both component and label, and optionally specifies layout
+ * constraints for the added component (but not the label)
*
- * @param panel
+ * @param container
* @param tooltip
* @param label
- * @param valBox
- * @return the GUI element created that was added to the layout so it's
- * attributes can be changed.
+ * @param comp
+ * @param constraints
*/
- public static JPanel addtoLayout(JPanel panel, String tooltip,
- JComponent label, JComponent valBox)
- {
- JPanel laypanel = new JPanel(new GridLayout(1, 2));
- JPanel labPanel = new JPanel(new BorderLayout());
- JPanel valPanel = new JPanel();
- labPanel.setBounds(new Rectangle(7, 7, 158, 23));
- valPanel.setBounds(new Rectangle(172, 7, 270, 23));
- labPanel.add(label, BorderLayout.WEST);
- valPanel.add(valBox);
- laypanel.add(labPanel);
- laypanel.add(valPanel);
- valPanel.setToolTipText(tooltip);
- labPanel.setToolTipText(tooltip);
- valBox.setToolTipText(tooltip);
- panel.add(laypanel);
- panel.validate();
- return laypanel;
- }
-
- public static void mgAddtoLayout(JPanel cpanel, String tooltip,
- JLabel jLabel, JComponent name)
+ public static void addtoLayout(Container container, String tooltip,
+ JComponent label, JComponent comp, String constraints)
{
- mgAddtoLayout(cpanel, tooltip, jLabel, name, null);
- }
-
- public static void mgAddtoLayout(JPanel cpanel, String tooltip,
- JLabel jLabel, JComponent name, String params)
- {
- cpanel.add(jLabel);
- if (params == null)
- {
- cpanel.add(name);
- }
- else
- {
- cpanel.add(name, params);
- }
- name.setToolTipText(tooltip);
- jLabel.setToolTipText(tooltip);
+ container.add(label);
+ container.add(comp, constraints);
+ comp.setToolTipText(tooltip); // this doesn't seem to show?
+ label.setToolTipText(tooltip);
}
/**
/**
* Adds a titled border to the component in the default font and position (top
- * left), optionally witht italic text
+ * left), optionally with italic text
*
* @param comp
* @param title
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.renderer.OverviewRenderer;
import jalview.util.MessageManager;
private OverviewCanvas oviewCanvas;
- protected AlignViewport av;
+ private AlignViewportI av;
private AlignmentPanel ap;
protected boolean draggingBox = false;
+ private Dimension dim;
+
+ private boolean showProgress = !Platform.isJS();
+
protected ProgressPanel progressPanel;
+
/**
- * Creates a new OverviewPanel object.
- *
- * @param alPanel
- * The alignment panel which is shown in the overview panel
+ * Creates the appropriate type of OverviewDimensions, with the desired size
*/
- public OverviewPanel(AlignmentPanel alPanel)
+ private void createOverviewDimensions()
{
- this.av = alPanel.av;
- this.ap = alPanel;
-
- showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
- false);
+ boolean showAnnotation = (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null);
if (showHidden)
{
- od = new OverviewDimensionsShowHidden(av.getRanges(),
- (av.isShowAnnotation()
- && av.getAlignmentConservationAnnotation() != null));
+ od = new OverviewDimensionsShowHidden(av.getRanges(), showAnnotation,
+ dim);
}
else
{
- od = new OverviewDimensionsHideHidden(av.getRanges(),
- (av.isShowAnnotation()
- && av.getAlignmentConservationAnnotation() != null));
+ od = new OverviewDimensionsHideHidden(av.getRanges(), showAnnotation,
+ dim);
}
+ }
+ public OverviewPanel(AlignmentPanel alPanel, Dimension dim)
+ {
+ this.av = alPanel.av;
+ this.ap = alPanel;
+ this.dim = dim;
+
+ showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+ false);
+ createOverviewDimensions();
setLayout(new BorderLayout());
progressPanel = new ProgressPanel(OverviewRenderer.UPDATE,
MessageManager.getString("label.oview_calc"), getWidth());
*/
protected void toggleHiddenColumns()
{
- if (showHidden)
- {
- showHidden = false;
- od = new OverviewDimensionsHideHidden(av.getRanges(),
- (av.isShowAnnotation()
- && av.getAlignmentConservationAnnotation() != null));
- }
- else
- {
- showHidden = true;
- od = new OverviewDimensionsShowHidden(av.getRanges(),
- (av.isShowAnnotation()
- && av.getAlignmentConservationAnnotation() != null));
- }
+ showHidden = !showHidden;
+ createOverviewDimensions();
oviewCanvas.resetOviewDims(od);
updateOverviewImage();
setBoxPosition();
import jalview.math.RotatableMatrix.Axis;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
+ import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
repaint();
if (getParent() == null)
{
- Desktop.addInternalFrame(this,
- MessageManager.formatMessage("label.calc_title", "PCA",
- getPcaModel().getScoreModelName()),
- 475, 450);
+ addToDesktop(this, getPcaModel().getScoreModelName());
this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
working = false;
// // setMenusForViewport();
// validate();
}
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ progressBar.removeProgressBar(id);
+ }
@Override
public void registerHandler(final long id,
getRotatableCanvas().ap = panel;
PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());
}
+
+ public static void addToDesktop(PCAPanel panel, String modelName)
+ {
+ Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
+ Desktop.addInternalFrame(panel, MessageManager.formatMessage(
+ "label.calc_title", "PCA", modelName), dim.width,
+ dim.height);
+ }
}
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.ResidueCount;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.CountReader;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
import jalview.util.UrlLink;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
/**
* The popup menu that is displayed on right-click on a sequence id, or in the
* sequence alignment.
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
JvOptionPane.WARNING_MESSAGE);
}
}
+ if (seq.hasHMMProfile())
+ {
+ menuItem = new JMenuItem(MessageManager
+ .getString("action.add_background_frequencies"));
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ ResidueCount counts = CountReader.getBackgroundFrequencies(ap,
+ seq);
+ if (counts != null)
+ {
+ seq.getHMM().setBackgroundFrequencies(counts);
+ ap.alignFrame.buildColourMenu();
+ }
+ } catch (MalformedURLException e1)
+ {
+ e1.printStackTrace();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ add(menuItem);
+ }
+
menuItem = new JMenuItem(
MessageManager.getString("action.hide_sequences"));
menuItem.addActionListener(new ActionListener()
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
+ Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
SequenceI sqass = null;
for (SequenceI sq : alignPanel.av.getSequenceSelection())
menuItem.setEnabled(true);
for (String calcId : tipEntries.keySet())
{
- tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
+ tooltip.append("<br>" + calcId + "/" + tipEntries.get(calcId));
}
String tooltipText = JvSwingUtils.wrapTooltip(true,
tooltip.toString());
ap.paintAlignment(false, false);
}
sequence.setDescription(dialog.getDescription());
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.notifyAlignment();
}
});
}
refresh();
}
};
- JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
+ JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
title, Color.BLUE, listener);
}
startEnd, caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
+ ap.av.notifyAlignment();
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
}
}
sg.getStartRes(), sg.getEndRes() + 1,
ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.notifyAlignment();
}
});
}
*/
package jalview.gui;
- import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
- import jalview.bin.Cache;
- import jalview.gui.Help.HelpId;
- import jalview.gui.StructureViewer.ViewerType;
- import jalview.hmmer.HmmerCommand;
- import jalview.io.BackupFiles;
- import jalview.io.BackupFilesPresetEntry;
- import jalview.io.FileFormatI;
- import jalview.io.JalviewFileChooser;
- import jalview.io.JalviewFileView;
- import jalview.jbgui.GPreferences;
- import jalview.jbgui.GSequenceLink;
- import jalview.schemes.ColourSchemeI;
- import jalview.schemes.ColourSchemes;
- import jalview.schemes.ResidueColourScheme;
- import jalview.urls.UrlLinkTableModel;
- import jalview.urls.api.UrlProviderFactoryI;
- import jalview.urls.api.UrlProviderI;
- import jalview.urls.desktop.DesktopUrlProviderFactory;
- import jalview.util.FileUtils;
- import jalview.util.MessageManager;
- import jalview.util.Platform;
- import jalview.util.UrlConstants;
- import jalview.ws.sifts.SiftsSettings;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.MouseEvent;
import java.io.File;
import java.util.ArrayList;
import javax.swing.JFileChooser;
import javax.swing.JInternalFrame;
import javax.swing.JPanel;
+import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
import javax.swing.RowFilter;
import javax.swing.RowSorter;
import javax.swing.table.TableModel;
import javax.swing.table.TableRowSorter;
++import jalview.hmmer.HmmerCommand;
++import jalview.util.FileUtils;
++
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+ import jalview.bin.Cache;
+ import jalview.gui.Help.HelpId;
+ import jalview.gui.StructureViewer.ViewerType;
+ import jalview.io.BackupFiles;
+ import jalview.io.BackupFilesPresetEntry;
+ import jalview.io.FileFormatI;
+ import jalview.io.JalviewFileChooser;
+ import jalview.io.JalviewFileView;
+ import jalview.jbgui.GPreferences;
+ import jalview.jbgui.GSequenceLink;
+ import jalview.schemes.ColourSchemeI;
+ import jalview.schemes.ColourSchemes;
+ import jalview.schemes.ResidueColourScheme;
+ import jalview.urls.UrlLinkTableModel;
+ import jalview.urls.api.UrlProviderFactoryI;
+ import jalview.urls.api.UrlProviderI;
+ import jalview.urls.desktop.DesktopUrlProviderFactory;
+ import jalview.util.MessageManager;
+ import jalview.util.Platform;
+ import jalview.util.UrlConstants;
+ import jalview.ws.sifts.SiftsSettings;
/**
* DOCUMENT ME!
*/
public class Preferences extends GPreferences
{
+ // suggested list delimiter character
+ public static final String COMMA = ",";
+
+ public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT";
+
+ public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND";
+
+ public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI";
+
+ public static final String ADD_SS_ANN = "ADD_SS_ANN";
- public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
+ public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
- public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+ public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING";
+
+ public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX";
+
+ public static final String ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN";
+
+ public static final String ANTI_ALIAS = "ANTI_ALIAS";
+
+ public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS";
+
+ public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
+
+ public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
+
+ public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
+
+ public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+ public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
+ public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+
public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
- public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+ public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
- public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+ public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
- public static final String ADD_SS_ANN = "ADD_SS_ANN";
+ public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
- public static final String USE_RNAVIEW = "USE_RNAVIEW";
+ public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS";
- public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+ public static final String FONT_NAME = "FONT_NAME";
- public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+ public static final String FONT_SIZE = "FONT_SIZE";
- public static final String CHIMERA_PATH = "CHIMERA_PATH";
+ public static final String FONT_STYLE = "FONT_STYLE";
+
+ public static final String HMMER_PATH = "HMMER_PATH";
+
+ public static final String CYGWIN_PATH = "CYGWIN_PATH";
+
+ public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
- public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+ public static final String GAP_COLOUR = "GAP_COLOUR";
+
+ public static final String GAP_SYMBOL = "GAP_SYMBOL";
+
+ public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
+ public static final String HIDE_INTRONS = "HIDE_INTRONS";
+
+ public static final String ID_ITALICS = "ID_ITALICS";
+
+ public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL";
+
+ public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS";
+
+ public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
+
+ public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO";
+
+ public static final String NORMALISE_LOGO = "NORMALISE_LOGO";
+
+ public static final String PAD_GAPS = "PAD_GAPS";
+
+ public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT";
+
+ public static final String QUESTIONNAIRE = "QUESTIONNAIRE";
+
+ public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING";
+
+ public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
+
+ public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+
+ public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+ public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
+
+ public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
+
+ public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO";
+
+ public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
+
+ public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP";
+
+ public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS";
+
+ public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
+
+ public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
+
+ public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
+
public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
+ public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
+
+ public static final String SHOW_QUALITY = "SHOW_QUALITY";
+
+ public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED";
+
+ public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
+
+ public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SORT_BY_TREE = "SORT_BY_TREE";
+
+ public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+ public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+ public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS";
+
+ public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN";
+
+ public static final String USE_FULL_SO = "USE_FULL_SO";
+
public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
- public static final String GAP_COLOUR = "GAP_COLOUR";
+ public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+ public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+
+ public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
- public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
private static final int MIN_FONT_SIZE = 1;
private WsPreferences wsPrefs;
+ private SlivkaPreferences slivkaPrefs;
+
private OptionsParam promptEachTimeOpt = new OptionsParam(
MessageManager.getString("label.prompt_each_time"),
"Prompt each time");
{
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
+ slivkaPrefs = new SlivkaPreferences();
+ slivkaTab.add(slivkaPrefs, BorderLayout.CENTER);
}
int width = 500, height = 450;
if (Platform.isAMacAndNotJS())
frame.setMinimumSize(new Dimension(width, height));
/*
+ * Set HMMER tab defaults
+ */
+ hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
+ if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+ hmmerPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateHmmerPath();
+ }
+ });
+ hmmerPath.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ validateHmmerPath();
+ }
+ });
+ if (cygwinPath != null)
+ {
+ String path = Cache.getProperty(CYGWIN_PATH);
+ if (path == null)
+ {
+ path = FileUtils.getPathTo("bash");
+ }
+ cygwinPath.setText(path);
+ cygwinPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateCygwinPath();
+ }
+ });
+ cygwinPath.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ validateCygwinPath();
+ }
+ });
+ }
+
+ /*
* Set Visual tab defaults
*/
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
showConsensLogo
.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ showInformationHistogram.setSelected(
+ Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
+ showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
showNpTooltip
.setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
showDbRefTooltip
addSecondaryStructure.setEnabled(structSelected);
addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
addTempFactor.setEnabled(structSelected);
- structViewer.setSelectedItem(
+ if (!Platform.isJS())
+ {
+ structViewer.setSelectedItem(
Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
+ }
chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
chimeraPath.addActionListener(new ActionListener()
{
doReset.addActionListener(onReset);
// filter to display only custom urls
- final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
+ final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
{
@Override
public boolean include(
/*
* Save Visual settings
*/
- Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
+ Cache.setPropertyNoSave("SHOW_JVSUFFIX",
Boolean.toString(seqLimit.isSelected()));
- Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
+ Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
Boolean.toString(rightAlign.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
+ Cache.setPropertyNoSave("SHOW_FULLSCREEN",
Boolean.toString(fullScreen.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
+ Cache.setPropertyNoSave("SHOW_OVERVIEW",
Boolean.toString(openoverv.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
Boolean.toString(annotations.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave("SHOW_CONSERVATION",
Boolean.toString(conservation.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Cache.setPropertyNoSave("SHOW_QUALITY",
Boolean.toString(quality.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Cache.setPropertyNoSave("SHOW_IDENTITY",
Boolean.toString(identity.isSelected()));
- Cache.applicationProperties.setProperty("GAP_SYMBOL",
+ Cache.setPropertyNoSave("GAP_SYMBOL",
gapSymbolCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_NAME",
+ Cache.setPropertyNoSave("FONT_NAME",
fontNameCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_STYLE",
+ Cache.setPropertyNoSave("FONT_STYLE",
fontStyleCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_SIZE",
+ Cache.setPropertyNoSave("FONT_SIZE",
fontSizeCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("ID_ITALICS",
+ Cache.setPropertyNoSave("ID_ITALICS",
Boolean.toString(idItalics.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
+ Cache.setPropertyNoSave("SHOW_UNCONSERVED",
Boolean.toString(showUnconserved.isSelected()));
- Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
+ Cache.setPropertyNoSave(SHOW_OCCUPANCY,
Boolean.toString(showOccupancy.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
+ Cache.setPropertyNoSave("SHOW_GROUP_CONSENSUS",
Boolean.toString(showGroupConsensus.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
+ Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION",
Boolean.toString(showGroupConservation.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
+ Cache.setPropertyNoSave("SHOW_CONSENSUS_HISTOGRAM",
Boolean.toString(showConsensHistogram.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
+ Cache.setPropertyNoSave("SHOW_CONSENSUS_LOGO",
Boolean.toString(showConsensLogo.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
++ Cache.setPropertyNoSave("SHOW_INFORMATION_HISTOGRAM",
+ Boolean.toString(showConsensHistogram.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
++ Cache.setPropertyNoSave("SHOW_HMM_LOGO",
+ Boolean.toString(showHMMLogo.isSelected()));
- Cache.applicationProperties.setProperty("ANTI_ALIAS",
+ Cache.setPropertyNoSave("ANTI_ALIAS",
Boolean.toString(smoothFont.isSelected()));
- Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
+ Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
Boolean.toString(scaleProteinToCdna.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
+ Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
Boolean.toString(showNpTooltip.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
+ Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
Boolean.toString(showDbRefTooltip.isSelected()));
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
+ Cache.setPropertyNoSave("WRAP_ALIGNMENT",
Boolean.toString(wrap.isSelected()));
- Cache.applicationProperties.setProperty("STARTUP_FILE",
+ Cache.setPropertyNoSave("STARTUP_FILE",
startupFileTextfield.getText());
- Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
+ Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
Boolean.toString(startupCheckbox.isSelected()));
- Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
+ Cache.setPropertyNoSave("SORT_ALIGNMENT",
sortby.getSelectedItem().toString());
// convert description of sort order to enum name for save
.forDescription(sortAnnBy.getSelectedItem().toString());
if (annSortOrder != null)
{
- Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
+ Cache.setPropertyNoSave(SORT_ANNOTATIONS,
annSortOrder.name());
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
- Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
+ Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
Boolean.valueOf(showAutocalcFirst).toString());
/*
* Save Colours settings
*/
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
+ Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
protColour.getSelectedItem().toString());
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
+ Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
nucColour.getSelectedItem().toString());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ Cache.setColourPropertyNoSave("ANNOTATIONCOLOUR_MIN",
minColour.getBackground());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ Cache.setColourPropertyNoSave("ANNOTATIONCOLOUR_MAX",
maxColour.getBackground());
/*
+ * Save HMMER settings
+ */
- Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI,
++ Cache.setPropertyNoSave(HMMALIGN_TRIM_TERMINI,
+ Boolean.toString(hmmrTrimTermini.isSelected()));
- Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND,
++ Cache.setPropertyNoSave(HMMINFO_GLOBAL_BACKGROUND,
+ Boolean.toString(hmmerBackgroundUniprot.isSelected()));
- Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT,
++ Cache.setPropertyNoSave(HMMSEARCH_SEQCOUNT,
+ hmmerSequenceCount.getText());
+ Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
+ if (cygwinPath != null)
+ {
+ Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
+ }
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames != null && frames.length > 0)
+ {
+ for (AlignFrame f : frames)
+ {
+ f.updateHMMERStatus();
+ }
+ }
+
+ hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
+ if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+
+ /*
* Save Overview settings
*/
- Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
- Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
- Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
+ Cache.setColourPropertyNoSave(GAP_COLOUR, gapColour.getBackground());
+ Cache.setColourPropertyNoSave(HIDDEN_COLOUR, hiddenColour.getBackground());
+ Cache.setPropertyNoSave(USE_LEGACY_GAP,
Boolean.toString(useLegacyGap.isSelected()));
- Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
+ Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
Boolean.toString(showHiddenAtStart.isSelected()));
/*
* Save Structure settings
*/
- Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+ Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
Boolean.toString(addTempFactor.isSelected()));
- Cache.applicationProperties.setProperty(ADD_SS_ANN,
+ Cache.setPropertyNoSave(ADD_SS_ANN,
Boolean.toString(addSecondaryStructure.isSelected()));
- Cache.applicationProperties.setProperty(USE_RNAVIEW,
+ Cache.setPropertyNoSave(USE_RNAVIEW,
Boolean.toString(useRnaView.isSelected()));
- Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+ Cache.setPropertyNoSave(STRUCT_FROM_PDB,
Boolean.toString(structFromPdb.isSelected()));
- Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
- structViewer.getSelectedItem().toString());
+ if (!Platform.isJS())
+ {
+ Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
+ structViewer.getSelectedItem().toString());
+ }
Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
- Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
+ Cache.setPropertyNoSave("MAP_WITH_SIFTS",
Boolean.toString(siftsMapping.isSelected()));
SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
/*
* Save Output settings
*/
- Cache.applicationProperties.setProperty("EPS_RENDERING",
+ Cache.setPropertyNoSave("EPS_RENDERING",
((OptionsParam) epsRendering.getSelectedItem()).getCode());
- Cache.applicationProperties.setProperty("HTML_RENDERING",
+ Cache.setPropertyNoSave("HTML_RENDERING",
((OptionsParam) htmlRendering.getSelectedItem()).getCode());
- Cache.applicationProperties.setProperty("SVG_RENDERING",
+ Cache.setPropertyNoSave("SVG_RENDERING",
((OptionsParam) svgRendering.getSelectedItem()).getCode());
/*
String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
if (menuLinks.isEmpty())
{
- Cache.applicationProperties.remove("SEQUENCE_LINKS");
+ Cache.removePropertyNoSave("SEQUENCE_LINKS");
}
else
{
- Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+ Cache.setPropertyNoSave("SEQUENCE_LINKS",
menuLinks.toString());
}
String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
if (nonMenuLinks.isEmpty())
{
- Cache.applicationProperties.remove("STORED_LINKS");
+ Cache.removePropertyNoSave("STORED_LINKS");
}
else
{
- Cache.applicationProperties.setProperty("STORED_LINKS",
+ Cache.setPropertyNoSave("STORED_LINKS",
nonMenuLinks.toString());
}
- Cache.applicationProperties.setProperty("DEFAULT_URL",
+ Cache.setPropertyNoSave("DEFAULT_URL",
sequenceUrlLinks.getPrimaryUrlId());
- Cache.applicationProperties.setProperty("USE_PROXY",
+ Cache.setPropertyNoSave("USE_PROXY",
Boolean.toString(useProxy.isSelected()));
Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
/*
* Save Output settings
*/
- Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
+ Cache.setPropertyNoSave("BLC_JVSUFFIX",
Boolean.toString(blcjv.isSelected()));
- Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
+ Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
Boolean.toString(clustaljv.isSelected()));
- Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
+ Cache.setPropertyNoSave("FASTA_JVSUFFIX",
Boolean.toString(fastajv.isSelected()));
- Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
+ Cache.setPropertyNoSave("MSF_JVSUFFIX",
Boolean.toString(msfjv.isSelected()));
- Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
+ Cache.setPropertyNoSave("PFAM_JVSUFFIX",
Boolean.toString(pfamjv.isSelected()));
- Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
+ Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
Boolean.toString(pileupjv.isSelected()));
- Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
+ Cache.setPropertyNoSave("PIR_JVSUFFIX",
Boolean.toString(pirjv.isSelected()));
- Cache.applicationProperties.setProperty("PIR_MODELLER",
+ Cache.setPropertyNoSave("PIR_MODELLER",
Boolean.toString(modellerOutput.isSelected()));
- Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
+ Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
Boolean.toString(embbedBioJSON.isSelected()));
jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
- Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
+ Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
- Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
+ Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
userIdWidth.getText());
/*
* Save Editing settings
*/
- Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+ Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
Boolean.toString(autoCalculateConsCheck.isSelected()));
- Cache.applicationProperties.setProperty("SORT_BY_TREE",
+ Cache.setPropertyNoSave("SORT_BY_TREE",
Boolean.toString(sortByTree.isSelected()));
- Cache.applicationProperties.setProperty("PAD_GAPS",
+ Cache.setPropertyNoSave("PAD_GAPS",
Boolean.toString(padGaps.isSelected()));
if (!Platform.isJS())
/*
* Save Backups settings
*/
- Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+ Cache.setPropertyNoSave(BackupFiles.ENABLED,
Boolean.toString(enableBackupFiles.isSelected()));
int preset = getComboIntStringKey(backupfilesPresetsCombo);
- Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
+ Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET", Integer.toString(preset));
if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
{
BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
- Cache.applicationProperties
- .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
+ Cache.setPropertyNoSave(BackupFilesPresetEntry.CUSTOMCONFIG,
customBFPE.toString());
}
BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
.get(preset);
- Cache.applicationProperties.setProperty(
+ Cache.setPropertyNoSave(
BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
Cache.saveProperties();
- Desktop.instance.doConfigureStructurePrefs();
+ Desktop.getInstance().doConfigureStructurePrefs();
try
{
frame.setClosed(true);
}
}
- /**
+ public static void setAppletDefaults()
+ {
+
+ // http://www.jalview.org/old/v2_8/examples/appletParameters.html
+
+ // showConservation true or false Default is true.
+ // showQuality true or false Default is true.
+ // showConsensus true or false Default is true.
+ // showFeatureSettings true or false Shows the feature settings window when
+ // startin
+ // showTreeBootstraps true or false (default is true) show or hide branch
+ // bootstraps
+ // showTreeDistances true or false (default is true) show or hide branch
+ // lengths
+ // showUnlinkedTreeNodes true or false (default is false) indicate if
+ // unassociated nodes should be highlighted in the tree view
+ // showUnconserved true of false (default is false) When true, only gaps and
+ // symbols different to the consensus sequence ions of the alignment
+ // showGroupConsensus true of false (default is false) When true, shows
+ // consensus annotation row for any groups on the alignment. (since 2.7)
+ // showGroupConservation true of false (default is false) When true, shows
+ // amino-acid property conservation annotation row for any groups on the
+ // showConsensusHistogram true of false (default is true) When true, shows
+ // the percentage occurence of the consensus symbol for each column as a
+ // showSequenceLogo true of false (default is false) When true, shows a
+ // sequence logo above the consensus sequence (overlaid above the Consensus
+
+ Cache.setPropertyNoSave(SHOW_CONSERVATION, "true");
+ Cache.setPropertyNoSave(SHOW_QUALITY, "false");
+ Cache.setPropertyNoSave(SHOW_CONSENSUS, "true");
+ Cache.setPropertyNoSave(SHOW_UNCONSERVED, "false");
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, "false");
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, "false");
+
+ // TODO -- just a start here
+ }
+ /**
* Do any necessary validation before saving settings. Return focus to the
* first tab which fails validation.
*
FileFormatI format = chooser.getSelectedFormat();
if (format != null)
{
- Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
+ Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
format.getName());
}
startupFileTextfield
&& (identity.isSelected() || showGroupConsensus.isSelected()));
showConsensLogo.setEnabled(annotations.isSelected()
&& (identity.isSelected() || showGroupConsensus.isSelected()));
+ showInformationHistogram.setEnabled(annotations.isSelected());
+ showHMMLogo.setEnabled(annotations.isSelected());
}
@Override
boolean valid = false;
while (!valid)
{
- if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
MessageManager.getString("label.new_sequence_url_link"),
JvOptionPane.OK_CANCEL_OPTION, -1,
null) == JvOptionPane.OK_OPTION)
boolean valid = false;
while (!valid)
{
- if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
MessageManager.getString("label.edit_sequence_url_link"),
JvOptionPane.OK_CANCEL_OPTION, -1,
null) == JvOptionPane.OK_OPTION)
} catch (NumberFormatException x)
{
userIdWidth.setText("");
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager
.getString("warn.user_defined_width_requirements"),
MessageManager.getString("label.invalid_id_column_width"),
File f = new File(chimeraPath.getText());
if (!f.canExecute())
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.invalid_chimera_path"),
MessageManager.getString("label.invalid_name"),
JvOptionPane.ERROR_MESSAGE);
}
return true;
}
+
+ /**
+ * Returns true if the given text field contains a path to a folder that
+ * contains an executable with the given name, else false (after showing a
+ * warning dialog). The executable name will be tried with .exe appended if not
+ * found.
+ *
+ * @param textField
+ * @param executable
+ */
+ protected boolean validateExecutablePath(JTextField textField, String executable)
+ {
+ String folder = textField.getText().trim();
+
+ if (FileUtils.getExecutable(executable, folder) != null)
+ {
+ return true;
+ }
+ if (folder.length() > 0)
+ {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
++ JvOptionPane.showInternalMessageDialog(Desktop.getInstance(),
+ MessageManager.formatMessage("label.executable_not_found",
+ executable),
+ MessageManager.getString("label.invalid_folder"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return false;
+ }
+
+ /**
+ * Checks if a file can be executed
+ *
+ * @param path
+ * the path to the file
+ * @return
+ */
+ public boolean canExecute(String path)
+ {
+ File file = new File(path);
+ if (!file.canExecute())
+ {
+ file = new File(path + ".exe");
+ {
+ if (!file.canExecute())
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
/**
* If Chimera is selected, check it can be found on default or user-specified
if (!found)
{
String[] options = { "OK", "Help" };
- int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+ int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
"", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
}
}
+ @Override
+ protected void validateHmmerPath()
+ {
+ validateExecutablePath(hmmerPath, HmmerCommand.HMMBUILD);
+ }
+
+ @Override
+ protected void validateCygwinPath()
+ {
+ validateExecutablePath(cygwinPath, "run");
+ }
+
public class OptionsParam
{
private String name;
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.api.SplitContainerI;
+import jalview.controller.FeatureSettingsControllerGuiI;
+import jalview.datamodel.AlignmentI;
+import jalview.jbgui.GAlignFrame;
+import jalview.jbgui.GSplitFrame;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
+
import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Dimension;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
-import jalview.api.AlignViewControllerGuiI;
-import jalview.api.FeatureSettingsControllerI;
-import jalview.api.SplitContainerI;
-import jalview.controller.FeatureSettingsControllerGuiI;
-import jalview.datamodel.AlignmentI;
-import jalview.jbgui.GAlignFrame;
-import jalview.jbgui.GSplitFrame;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.AlignmentViewport;
-
/**
* An internal frame on the desktop that hosts a horizontally split view of
* linked DNA and Protein alignments. Additional views can be created in linked
// allow about 65 pixels for Desktop decorators on Windows
int newHeight = Math.min(height,
- Desktop.instance.getHeight() - DESKTOP_DECORATORS_HEIGHT);
+ Desktop.getInstance().getHeight() - DESKTOP_DECORATORS_HEIGHT);
if (newHeight != height)
{
int oldDividerLocation = getDividerLocation();
// TODO if CommandListener is only ever 1:1 for complementary views,
// may change broadcast pattern to direct messaging (more efficient)
final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
}
topFrame.alignPanel.adjustAnnotationHeight();
bottomFrame.alignPanel.adjustAnnotationHeight();
- final AlignViewport topViewport = topFrame.viewport;
- final AlignViewport bottomViewport = bottomFrame.viewport;
+ final AlignViewportI topViewport = topFrame.viewport;
+ final AlignViewportI bottomViewport = bottomFrame.viewport;
final AlignmentI topAlignment = topViewport.getAlignment();
final AlignmentI bottomAlignment = bottomViewport.getAlignment();
boolean topAnnotations = topViewport.isShowAnnotation();
* Ctrl-W / Cmd-W - close view or window
*/
KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
action = new AbstractAction()
{
@Override
* Ctrl-T / Cmd-T open new view
*/
KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
AbstractAction action = new AbstractAction()
{
@Override
adjustLayout();
final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.addCommandListener(newTopPanel.av);
ssm.addCommandListener(newBottomPanel.av);
}
*/
protected void expandViews_actionPerformed()
{
- Desktop.instance.explodeViews(this);
+ Desktop.getInstance().explodeViews(this);
}
/**
*/
protected void gatherViews_actionPerformed()
{
- Desktop.instance.gatherViews(this);
+ Desktop.getInstance().gatherViews(this);
}
/**
* Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
*/
KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
AbstractAction action = new AbstractAction()
{
@Override
{
return featureSettingsUI != null && !featureSettingsUI.isClosed();
}
-}
+}
package jalview.gui;
- import jalview.api.structures.JalviewStructureDisplayI;
- import jalview.bin.Cache;
- import jalview.bin.Jalview;
- import jalview.datamodel.DBRefEntry;
- import jalview.datamodel.DBRefSource;
- import jalview.datamodel.PDBEntry;
- import jalview.datamodel.SequenceI;
- import jalview.fts.api.FTSData;
- import jalview.fts.api.FTSDataColumnI;
- 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;
- import jalview.ws.sifts.SiftsSettings;
-
import java.awt.event.ItemEvent;
import java.util.ArrayList;
import java.util.Collection;
import javax.swing.SwingUtilities;
import javax.swing.table.AbstractTableModel;
+ import jalview.api.structures.JalviewStructureDisplayI;
+ import jalview.bin.Cache;
+ import jalview.bin.Jalview;
+ import jalview.datamodel.DBRefEntry;
+ import jalview.datamodel.DBRefSource;
+ import jalview.datamodel.PDBEntry;
+ import jalview.datamodel.SequenceI;
+ import jalview.fts.api.FTSData;
+ import jalview.fts.api.FTSDataColumnI;
+ 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.util.MessageManager;
+
/**
* Provides the behaviors for the Structure chooser Panel
*
public class StructureChooser extends GStructureChooser
implements IProgressIndicator
{
- private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
+ static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
private static int MAX_QLENGTH = 7820;
private boolean cachedPDBExists;
- private static StructureViewer lastTargetedView = null;
+ static StructureViewer lastTargetedView = null;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
*/
private void discoverStructureViews()
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
targetView.removeAllItems();
if (lastTargetedView != null && !lastTargetedView.isVisible())
lastTargetedView = null;
}
int linkedViewsAt = 0;
- for (StructureViewerBase view : Desktop.instance
+ for (StructureViewerBase view : Desktop.getInstance()
.getStructureViewers(null, null))
{
StructureViewer viewHandler = (lastTargetedView != null
if (view.isLinkedWith(ap))
{
- targetView.insertItemAt(viewHandler,
- linkedViewsAt++);
+ targetView.insertItemAt(viewHandler, linkedViewsAt++);
}
else
{
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
Set<String> seqRefs = new LinkedHashSet<>();
-
+
/*
* note PDBs as DBRefEntry so they are not duplicated in query
*/
{
for (int ib = 0, nb = refs.size(); ib < nb; ib++)
{
- DBRefEntry dbRef = refs.get(ib);
+ DBRefEntry dbRef = refs.get(ib);
if (isValidSeqName(getDBRefId(dbRef))
&& queryBuilder.length() < MAX_QLENGTH)
{
@Override
protected void pdbFromFile_actionPerformed()
{
- // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser
+ // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and
+ // StructureChooser
// works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
if (cachedPDBExist)
{
FilterOption cachedOption = new FilterOption(
- MessageManager.getString("label.cached_structures"),
- "-", VIEWS_LOCAL_PDB, false);
+ MessageManager.getString("label.cached_structures"), "-",
+ VIEWS_LOCAL_PDB, false);
cmb_filterOption.addItem(cachedOption);
cmb_filterOption.setSelectedItem(cachedOption);
}
}
return found;
}
-
+
/**
* Handles the 'New View' action
*/
public void showStructures(boolean waitUntilFinished)
{
- final StructureSelectionManager ssm = ap.getStructureSelectionManager();
-
final int preferredHeight = pnl_filter.getHeight();
+ final StructureViewer theViewer = getTargetedStructureViewer();
+ boolean superimpose = chk_superpose.isSelected();
+
Runnable viewStruc = new Runnable()
{
@Override
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = restable.getColumn("PDB Id")
- .getModelIndex();
+ int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
int refSeqColIndex = restable.getColumn("Ref Sequence")
.getModelIndex();
int[] selectedRows = restable.getSelectedRows();
List<SequenceI> selectedSeqsToView = new ArrayList<>();
for (int row : selectedRows)
{
- String pdbIdStr = restable
- .getValueAt(row, pdbIdColIndex).toString();
- SequenceI selectedSeq = (SequenceI) restable
- .getValueAt(row, refSeqColIndex);
+ String pdbIdStr = restable.getValueAt(row, pdbIdColIndex)
+ .toString();
+ SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
+ refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
if (pdbEntry == null)
{
- pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
+ pdbEntry = new PDBEntry(pdbIdStr, null, "pdb");
selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
}
pdbEntriesToView[count++] = pdbEntry;
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs, superimpose, theViewer, progressBar);
}
else if (currentView == VIEWS_LOCAL_PDB)
{
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
+ selectedSeqs, superimpose, theViewer, progressBar);
}
else if (currentView == VIEWS_ENTER_ID)
{
}
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ sViewer = StructureViewer.launchStructureViewer(ap, pdbEntriesToView,
new SequenceI[]
- { selectedSequence });
+ { selectedSequence }, superimpose, theViewer,
+ progressBar);
}
else if (currentView == VIEWS_FROM_FILE)
{
{
selectedSequence = userSelectedSeq;
}
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- DataSourceType.FILE, selectedSequence, true,
- Desktop.instance);
-
- sViewer = launchStructureViewer(
- ssm, new PDBEntry[]
- { fileEntry }, ap,
+ PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName,
+ DataSourceType.FILE, selectedSequence, true);
+ sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry },
new SequenceI[]
- { selectedSequence });
+ { selectedSequence }, superimpose, theViewer,
+ progressBar);
}
SwingUtilities.invokeLater(new Runnable()
{
* @param ssm
* @return
*/
- StructureViewer getTargetedStructureViewer(
- StructureSelectionManager ssm)
- {
- Object sv = targetView.getSelectedItem();
-
- return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
- }
-
- /**
- * Adds PDB structures to a new or existing structure viewer
- *
- * @param ssm
- * @param pdbEntriesToView
- * @param alignPanel
- * @param sequences
- * @return
- */
- private StructureViewer launchStructureViewer(
- StructureSelectionManager ssm,
- final PDBEntry[] pdbEntriesToView,
- final AlignmentPanel alignPanel, SequenceI[] sequences)
+ StructureViewer getTargetedStructureViewer()
{
- long progressId = sequences.hashCode();
- setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"), progressId);
- final StructureViewer theViewer = getTargetedStructureViewer(ssm);
- boolean superimpose = chk_superpose.isSelected();
- theViewer.setSuperpose(superimpose);
-
- /*
- * remember user's choice of superimpose or not
- */
- Cache.setProperty(AUTOSUPERIMPOSE,
- Boolean.valueOf(superimpose).toString());
-
- setProgressBar(null, progressId);
- if (SiftsSettings.isMapWithSifts())
- {
- List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
- int p = 0;
- // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
- // real PDB ID. For moment, we can also safely do this if there is already
- // a known mapping between the PDBEntry and the sequence.
- for (SequenceI seq : sequences)
- {
- PDBEntry pdbe = pdbEntriesToView[p++];
- if (pdbe != null && pdbe.getFile() != null)
- {
- StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
- if (smm != null && smm.length > 0)
- {
- for (StructureMapping sm : smm)
- {
- if (sm.getSequence() == seq)
- {
- continue;
- }
- }
- }
- }
- if (seq.getPrimaryDBRefs().isEmpty())
- {
- seqsWithoutSourceDBRef.add(seq);
- continue;
- }
- }
- if (!seqsWithoutSourceDBRef.isEmpty())
- {
- int y = seqsWithoutSourceDBRef.size();
- setProgressBar(MessageManager.formatMessage(
- "status.fetching_dbrefs_for_sequences_without_valid_refs",
- y), progressId);
- SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
- .toArray(new SequenceI[y]);
- DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
- dbRefFetcher.fetchDBRefs(true);
-
- setProgressBar("Fetch complete.", progressId); // todo i18n
- }
- }
- if (pdbEntriesToView.length > 1)
- {
- setProgressBar(MessageManager.getString(
- "status.fetching_3d_structures_for_selected_entries"),
- progressId);
- theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
- }
- else
- {
- setProgressBar(MessageManager.formatMessage(
- "status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()),progressId);
- theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
- }
- setProgressBar(null, progressId);
- // remember the last viewer we used...
- lastTargetedView = theViewer;
- return theViewer;
+ return (StructureViewer) targetView.getSelectedItem();
}
/**
&& !discoveredStructuresSet.isEmpty();
}
- protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes this.
+ protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes
+ // this.
// Doing a search for "1" or "1c" is valuable?
// Those work but are enormously slow.
protected void txt_search_ActionPerformed()
{
String text = txt_search.getText().trim();
- if (text.length() >= PDB_ID_MIN)
- new Thread()
- {
-
- @Override
- public void run()
+ if (text.length() >= PDB_ID_MIN)
+ new Thread()
{
- errorWarning.setLength(0);
- isValidPBDEntry = false;
- if (text.length() > 0)
+
+ @Override
+ public void run()
{
- String searchTerm = text.toLowerCase();
- searchTerm = searchTerm.split(":")[0];
- // System.out.println(">>>>> search term : " + searchTerm);
- List<FTSDataColumnI> wantedFields = new ArrayList<>();
- FTSRestRequest pdbRequest = new FTSRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(pdb_id:");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(searchTerm + ")");
- pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestClient = PDBFTSRestClient.getInstance();
- wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
- FTSRestResponse resultList;
- try
- {
- resultList = pdbRestClient.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- errorWarning.append(e.getMessage());
- return;
- } finally
- {
- validateSelections();
- }
- if (resultList.getSearchSummary() != null
- && resultList.getSearchSummary().size() > 0)
+ errorWarning.setLength(0);
+ isValidPBDEntry = false;
+ if (text.length() > 0)
{
- isValidPBDEntry = true;
+ String searchTerm = text.toLowerCase();
+ searchTerm = searchTerm.split(":")[0];
+ // System.out.println(">>>>> search term : " + searchTerm);
+ List<FTSDataColumnI> wantedFields = new ArrayList<>();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(pdb_id:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(searchTerm + ")");
+ pdbRequest.setAssociatedSequence(selectedSequence);
+ pdbRestClient = PDBFTSRestClient.getInstance();
+ wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = pdbRestClient.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errorWarning.append(e.getMessage());
+ return;
+ } finally
+ {
+ validateSelections();
+ }
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ isValidPBDEntry = true;
+ }
}
+ validateSelections();
}
- validateSelections();
- }
- }.start();
+ }.start();
}
@Override
{
progressBar.setProgressBar(message, id);
}
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ progressBar.removeProgressBar(id);
+ }
@Override
public void registerHandler(long id, IProgressIndicatorHandler handler)
{
return sViewer == null ? null : sViewer.sview;
}
+
}
public WebserviceInfo(String title, String info, int width, int height,
boolean makeVisible)
{
+ // no references
init(title, info, width, height, makeVisible);
}
{
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, title, makeVisible, width, height);
+ Desktop.addInternalFrame(frame, title, makeVisible, width, height, Desktop.FRAME_ALLOW_RESIZE, Desktop.FRAME_SET_MIN_SIZE_300);
frame.setClosable(false);
progressBar = new ProgressBar(statusPanel, statusBar);
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), message,
title, JvOptionPane.WARNING_MESSAGE);
}
{
progressBar.setProgressBar(message, id);
}
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ progressBar.removeProgressBar(id);
+ }
@Override
public void registerHandler(final long id,
import jalview.gui.OptsAndParamsPage.OptionBox;
import jalview.gui.OptsAndParamsPage.ParamBox;
import jalview.util.MessageManager;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.api.UIinfo;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.OptionI;
import jalview.ws.params.ParamDatastoreI;
import java.awt.event.HierarchyEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
-import java.awt.event.WindowEvent;
-import java.awt.event.WindowListener;
-import java.net.URL;
import java.util.Hashtable;
-import java.util.Iterator;
import java.util.List;
import java.util.Vector;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JDialog;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
import javax.swing.JTextArea;
import javax.swing.border.TitledBorder;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
-import compbio.metadata.Argument;
-import compbio.metadata.Option;
-import compbio.metadata.Parameter;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import compbio.metadata.RunnerConfig;
import net.miginfocom.swing.MigLayout;
/**
public class WsJobParameters extends JPanel implements ItemListener,
ActionListener, DocumentListener, OptsParametersContainerI
{
- URL linkImageURL = getClass().getResource("/images/link.gif");
+ private static final int PREFERRED_WIDTH = 540;
- private static final String SVC_DEF = "Defaults"; // this is the null
- // parameter set as shown to
- // user
+ private static final int DEFAULT_HEIGHT = 640;
+
+ // the default parameter set shown to the user
+ private static final String SVC_DEF = "Defaults";
+
+ private int maxOptWidth = 200;
+
+ // URL linkImageURL = getClass().getResource("/images/link.gif");
+
+ // TODO ABSRACT FROM JABAWS CLASSES
/**
* manager for options and parameters.
*/
- OptsAndParamsPage opanp = new OptsAndParamsPage(this);
+ OptsAndParamsPage opanp;
- /**
+ /*
* panel containing job options
*/
- JPanel jobOptions = new JPanel();
+ JPanel optionsPanel = new JPanel();
- /**
+ /*
* panel containing job parameters
*/
- JPanel paramList = new JPanel();
-
- JPanel SetNamePanel = new JPanel();
-
- JPanel setDetails = new JPanel();
-
- JSplitPane settingsPanel = new JSplitPane();
-
- JPanel jobPanel = new JPanel();
+ JPanel paramsPanel = new JPanel();
- JScrollPane jobOptionsPane = new JScrollPane();
+ JPanel setNamePanel = new JPanel();
JButton createpref = new JButton();
JButton updatepref = new JButton();
- JButton startjob = new JButton();
-
- JButton canceljob = new JButton();
-
- JComboBox setName = new JComboBox();
+ JComboBox<String> setName = new JComboBox<>();
JTextArea setDescr = new JTextArea();
JScrollPane paramPane = new JScrollPane();
- // ScrollablePanel optsAndparams = new ScrollablePanel();
- JPanel optsAndparams = new JPanel();
-
- RunnerConfig serviceOptions;
-
ParamDatastoreI paramStore;
- private int MAX_OPTWIDTH = 200;
+ // set true when 'Start Job' is clicked
+ boolean startJob = false;
- WsJobParameters(Jws2Instance service)
- {
- this(service, null);
- }
+ JDialog frame = null;
- public WsJobParameters(Jws2Instance service, WsParamSetI preset)
- {
- this(null, service, preset, null);
- }
+ UIinfo service;
- /**
- *
- * @param desktop
- * - if null, create new JFrame outside of desktop
- * @param service
- * @param preset
+ /*
+ * list of service presets in the gui
+ */
+ Hashtable<String, String> servicePresets = null;
+
+ /*
+ * set if dialog is being set - so handlers will avoid spurious events
*/
- public WsJobParameters(JFrame parent, Jws2Instance service,
- WsParamSetI preset, List<Argument> jobArgset)
+ boolean settingDialog = false;
+
+ private Hashtable<Object, Object> modifiedElements = new Hashtable<>();
+
+ String lastParmSet = null;
+
+ public WsJobParameters(ParamDatastoreI store, WsParamSetI preset,
+ List<ArgumentI> args)
{
- this(parent, null, service, preset, jobArgset);
+ super();
+
+ // parameters dialog in 'compact' format (help as tooltips)
+ opanp = new OptsAndParamsPage(this, true);
+ jbInit();
+ this.paramStore = store;
+ this.service = null;
+ init(preset, args);
+ validate();
}
/**
+ * Constructor given a set of parameters and presets, a service to be invoked,
+ * and a list of (Jabaws client) arguments
*
- * @param parent
* @param paramStorei
* @param service
* @param preset
* @param jobArgset
*/
- public WsJobParameters(JFrame parent, ParamDatastoreI paramStorei,
- Jws2Instance service, WsParamSetI preset,
- List<Argument> jobArgset)
+ public WsJobParameters(ParamDatastoreI paramStorei, UIinfo service,
+ WsParamSetI preset, List<ArgumentI> jobArgset)
{
super();
+
+ // parameters dialog in 'expanded' format (help text boxes)
+ opanp = new OptsAndParamsPage(this, false);
+
jbInit();
this.paramStore = paramStorei;
- if (paramStore == null)
+ if (paramStore == null && service != null)
{
paramStore = service.getParamStore();
}
this.service = service;
- // argSetModified(false);
- // populate parameter table
- initForService(service, preset, jobArgset);
- // display in new JFrame attached to parent.
+ initForService(preset, jobArgset);
validate();
}
- int response = -1;
-
- JDialog frame = null;
-
/**
- * shows a modal dialog containing the parameters.
+ * Shows a modal dialog containing the parameters and Start or Cancel options.
+ * Answers true if the job is started, false if cancelled.
*
* @return
*/
public boolean showRunDialog()
{
- frame = new JDialog(Desktop.instance, true);
+ frame = new JDialog(Desktop.getInstance(), true);
-
+ if (service != null)
+ {
+ frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
+ new String[]
+ { service.getActionText() }));
+ }
-
- Rectangle deskr = Desktop.instance.getBounds();
+ frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
+ new String[]
+ { service.getActionText() }));
+ Rectangle deskr = Desktop.getInstance().getBounds();
Dimension pref = this.getPreferredSize();
frame.setBounds(
new Rectangle((int) (deskr.getCenterX() - pref.width / 2),
});
frame.setVisible(true);
- if (response > 0)
- {
- return true;
- }
- return false;
+ return startJob;
}
private void jbInit()
@Override
public void actionPerformed(ActionEvent e)
{
- update_actionPerformed(e);
+ update_actionPerformed();
}
});
deletepref = JvSwingUtils.makeButton(
@Override
public void actionPerformed(ActionEvent e)
{
- delete_actionPerformed(e);
+ delete_actionPerformed();
}
});
createpref = JvSwingUtils.makeButton(
@Override
public void actionPerformed(ActionEvent e)
{
- create_actionPerformed(e);
+ create_actionPerformed();
}
});
revertpref = JvSwingUtils.makeButton(
@Override
public void actionPerformed(ActionEvent e)
{
- revert_actionPerformed(e);
+ revert_actionPerformed();
}
});
- startjob = JvSwingUtils.makeButton(
+
+ JButton startjob = JvSwingUtils.makeButton(
MessageManager.getString("action.start_job"),
MessageManager.getString("label.start_job_current_settings"),
new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- startjob_actionPerformed(e);
+ startjob_actionPerformed();
}
});
- canceljob = JvSwingUtils.makeButton(
+ JButton canceljob = JvSwingUtils.makeButton(
MessageManager.getString("action.cancel_job"),
MessageManager.getString("label.cancel_job_close_dialog"),
new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- canceljob_actionPerformed(e);
+ canceljob_actionPerformed();
}
});
+ JPanel setDetails = new JPanel();
setDetails.setBorder(
new TitledBorder(MessageManager.getString("label.details")));
setDetails.setLayout(new BorderLayout());
setName.getEditor().addActionListener(this);
JPanel setNameInfo = new JPanel(new FlowLayout(FlowLayout.LEFT));
GridBagLayout gbl = new GridBagLayout();
- SetNamePanel.setLayout(gbl);
+ setNamePanel.setLayout(gbl);
JLabel setNameLabel = new JLabel(
MessageManager.getString("label.current_parameter_set_name"));
revertpref.setVisible(false);
createpref.setVisible(false);
JPanel setsavebuts = new JPanel();
- setsavebuts.setLayout(new FlowLayout(FlowLayout.LEFT)); // GridLayout(1,2));
- ((FlowLayout) setsavebuts.getLayout()).setHgap(10);
- ((FlowLayout) setsavebuts.getLayout()).setVgap(0);
+ setsavebuts.setLayout(new FlowLayout(FlowLayout.LEFT, 10, 0)); // GridLayout(1,2));
JPanel spacer = new JPanel();
spacer.setPreferredSize(new Dimension(2, 30));
setsavebuts.add(spacer);
// setsavebuts.setSize(new Dimension(150, 30));
JPanel buttonArea = new JPanel(new GridLayout(1, 1));
buttonArea.add(setsavebuts);
- SetNamePanel.add(setNameInfo);
+ setNamePanel.add(setNameInfo);
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridheight = 2;
gbl.setConstraints(setNameInfo, gbc);
- SetNamePanel.add(buttonArea);
+ setNamePanel.add(buttonArea);
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 2;
// paramPane.setPreferredSize(new Dimension(360, 400));
// paramPane.setPreferredSize(null);
- jobOptions.setBorder(
+ optionsPanel.setBorder(
new TitledBorder(MessageManager.getString("label.options")));
- jobOptions.setOpaque(true);
- paramList.setBorder(
+ optionsPanel.setOpaque(true);
+ paramsPanel.setBorder(
new TitledBorder(MessageManager.getString("label.parameters")));
- paramList.setOpaque(true);
- JPanel bjo = new JPanel(new BorderLayout()),
- bjp = new JPanel(new BorderLayout());
- bjo.add(jobOptions, BorderLayout.CENTER);
- bjp.add(paramList, BorderLayout.CENTER);
- bjp.setOpaque(true);
- bjo.setOpaque(true);
+ paramsPanel.setOpaque(true);
// optsAndparams.setScrollableWidth(ScrollableSizeHint.FIT);
// optsAndparams.setScrollableHeight(ScrollableSizeHint.NONE);
// optsAndparams.setLayout(new BorderLayout());
+ JPanel optsAndparams = new JPanel();
optsAndparams.setLayout(new BorderLayout());
- optsAndparams.add(jobOptions, BorderLayout.NORTH);
- optsAndparams.add(paramList, BorderLayout.CENTER);
+ optsAndparams.add(optionsPanel, BorderLayout.NORTH);
+ optsAndparams.add(paramsPanel, BorderLayout.CENTER);
JPanel jp = new JPanel(new BorderLayout());
jp.add(optsAndparams, BorderLayout.CENTER);
paramPane.getViewport().setView(jp);
paramPane.setBorder(null);
setLayout(new BorderLayout());
+
+ JPanel jobPanel = new JPanel();
jobPanel.setPreferredSize(null);
jobPanel.setLayout(new BorderLayout());
jobPanel.add(setDetails, BorderLayout.NORTH);
jobPanel.add(paramPane, BorderLayout.CENTER);
// jobPanel.setOrientation(JSplitPane.VERTICAL_SPLIT);
- add(SetNamePanel, BorderLayout.NORTH);
+ add(setNamePanel, BorderLayout.NORTH);
add(jobPanel, BorderLayout.CENTER);
JPanel dialogpanel = new JPanel();
dialogpanel.add(canceljob);
// JAL-1580: setMaximumSize() doesn't work, so just size for the worst case:
// check for null is for JUnit usage
- final int windowHeight = Desktop.instance == null ? DEFAULT_HEIGHT
- : Desktop.instance.getHeight();
- // setPreferredSize(new Dimension(PREFERRED_WIDTH, windowHeight));
- final int windowHeight = Desktop.getInstance() == null ? 540
++ final int windowHeight = Desktop.getInstance() == null ? DEFAULT_HEIGHT
+ : Desktop.getInstance().getHeight();
+ setPreferredSize(new Dimension(540, windowHeight));
add(dialogpanel, BorderLayout.SOUTH);
validate();
}
- protected void revert_actionPerformed(ActionEvent e)
+ protected void revert_actionPerformed()
{
reInitDialog(lastParmSet);
updateWebServiceMenus();
}
- protected void update_actionPerformed(ActionEvent e)
+ protected void update_actionPerformed()
{
if (isUserPreset)
{
paramStore.deletePreset(lastParmSet2);
}
- protected void delete_actionPerformed(ActionEvent e)
+ protected void delete_actionPerformed()
{
if (isUserPreset)
{
updateWebServiceMenus();
}
- protected void create_actionPerformed(ActionEvent e)
+ protected void create_actionPerformed()
{
String curname = ((String) setName.getSelectedItem()).trim();
if (curname.length() > 0)
}
}
- protected void canceljob_actionPerformed(ActionEvent e)
+ protected void canceljob_actionPerformed()
{
- response = 0;
+ startJob = false;
if (frame != null)
{
frame.setVisible(false);
}
}
- protected void startjob_actionPerformed(ActionEvent e)
+ protected void startjob_actionPerformed()
{
- response = 1;
+ startJob = true;
if (frame != null)
{
frame.setVisible(false);
}
}
- Jws2Instance service;
+ void initForService(WsParamSetI paramSet, List<ArgumentI> jobArgset)
+ {
+ settingDialog = true;
- /**
- * list of service presets in the gui
- */
- Hashtable servicePresets = null;
+ init(paramSet, jobArgset);
- /**
- * set if dialog is being set - so handlers will avoid spurious events
- */
- boolean settingDialog = false;
+ }
- void initForService(Jws2Instance service, WsParamSetI jabap,
- List<Argument> jabajobArgset)
+ void init(WsParamSetI p, List<ArgumentI> jobArgset)
{
- WsParamSetI p = null;
- List<ArgumentI> jobArgset = null;
- settingDialog = true;
- { // instantiate the abstract proxy for Jaba objects
- jobArgset = jabajobArgset == null ? null
- : JabaParamStore.getJwsArgsfromJaba(jabajobArgset);
- p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
- // null;
- }
-
- Hashtable exnames = new Hashtable();
+ Hashtable<String, String> exnames = new Hashtable<>();
for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
{
exnames.put(setName.getItemAt(i), setName.getItemAt(i));
}
- servicePresets = new Hashtable();
+ servicePresets = new Hashtable<>();
// Add the default entry - if not present already.
if (!exnames.contains(SVC_DEF))
{
exnames.put(SVC_DEF, SVC_DEF);
servicePresets.put(SVC_DEF, SVC_DEF);
}
- String curname = (p == null ? "" : p.getName());
+
+ // String curname = (p == null ? "" : p.getName());
for (WsParamSetI pr : paramStore.getPresets())
{
if (!pr.isModifiable())
}
}
settingDialog = false;
-
}
- @SuppressWarnings("unchecked")
private void updateTable(WsParamSetI p, List<ArgumentI> jobArgset)
{
boolean setDefaultParams = false;
OptionI opt = (OptionI) myarg;
OptionBox ob = opanp.addOption(opt);
ob.resetToDefault(setDefaultParams);
- if (MAX_OPTWIDTH < ob.getPreferredSize().width)
+ if (maxOptWidth < ob.getPreferredSize().width)
{
- MAX_OPTWIDTH = ob.getPreferredSize().width;
+ maxOptWidth = ob.getPreferredSize().width;
}
ob.validate();
cw += ob.getPreferredSize().width + 5;
return modifiedElements.size() > 0;
}
- private Hashtable modifiedElements = new Hashtable();
-
/**
* reset gui and modification state settings
*/
if (b && modifiedElements.size() > 0)
{
makeSetNameValid(!isUserPreset);
- SetNamePanel.revalidate();
+ setNamePanel.revalidate();
}
updateButtonDisplay();
}
// sync the gui with the preset database
for (int i = 0, iS = setName.getItemCount(); i < iS; i++)
{
- String snm = (String) setName.getItemAt(i);
+ String snm = setName.getItemAt(i);
if (snm.equals(nm))
{
makeupdate = true;
settingDialog = stn;
}
+ /**
+ * Rebuilds the Options and Parameters panels
+ */
@Override
public void refreshParamLayout()
{
- // optsAndparams.setPreferredSize(null);
- FlowLayout fl = new FlowLayout(FlowLayout.LEFT);
- int sep = fl.getVgap();
- boolean fh = true;
- int os = 0,
- s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom
- + jobOptions.getBorder().getBorderInsets(jobOptions).top
- + 2 * sep;
- /**
- * final height for viewport
- */
- int finalh = s;
- int panewidth = paramPane.getViewport().getSize().width - 120
- - jobOptions.getBorder().getBorderInsets(jobOptions).left
- + jobOptions.getBorder().getBorderInsets(jobOptions).right;
-
- int w = 2 * fl.getHgap()
- + (MAX_OPTWIDTH > OptsAndParamsPage.PARAM_WIDTH ? MAX_OPTWIDTH
- : OptsAndParamsPage.PARAM_WIDTH);
- int hgap = fl.getHgap(), cw = hgap;
+ final int rightMargin = 40;
+ final int availableWidth = paramPane.getViewport().getSize().width
+ - rightMargin
+ - optionsPanel.getBorder().getBorderInsets(optionsPanel).left
+ + optionsPanel.getBorder().getBorderInsets(optionsPanel).right;
if (opanp.getOptSet().size() > 0)
{
+ int hgap = 5;
+ int currentWidth = hgap;
- jobOptions.setLayout(new MigLayout("", "", ""));
- jobOptions.removeAll();
+ /*
+ * layout constraint 'nogrid' prevents vertical column alignment,
+ * allowing controls to flow without extra space inserted to align
+ */
+ optionsPanel.setLayout(new MigLayout("nogrid", "", ""));
+ optionsPanel.removeAll();
+ JPanel lastAdded = null;
+ /*
+ * add each control in turn; if adding would overflow the right margin,
+ * remove and re-add the previous parameter with "wrap" (after)
+ * in order to start a new row
+ */
for (OptionBox pbox : opanp.getOptSet().values())
{
pbox.validate();
- cw += pbox.getSize().width + hgap;
- if (cw + 120 > panewidth)
- {
- jobOptions.add(pbox, "wrap");
- // System.out.println("Wrap on "+pbox.option.getName());
- cw = hgap + pbox.getSize().width;
- fh = true;
- }
- else
- {
- jobOptions.add(pbox);
- }
- if (fh)
+ int boxWidth = pbox.getSize().width;
+ currentWidth += boxWidth + hgap;
+ boolean wrapAfterLast = currentWidth > availableWidth
+ && lastAdded != null;
+ // System.out.println(String.format(
+ // "%s width=%d, paneWidth=%d, currentWidth=%d, wrapAfterLast=%s",
+ // pbox.toString(), boxWidth, panewidth, currentWidth,
+ // wrapAfterLast));
+ if (wrapAfterLast)
{
- finalh += pbox.getSize().height + fl.getVgap();
- fh = false;
+ optionsPanel.remove(lastAdded);
+ optionsPanel.add(lastAdded, "wrap");
+ currentWidth = hgap + boxWidth;
}
+ optionsPanel.add(pbox);
+ lastAdded = pbox;
}
- jobOptions.revalidate();
+ optionsPanel.revalidate();
}
else
{
- jobOptions.setVisible(false);
+ optionsPanel.setVisible(false);
}
- // Now layout the parameters assuming they occupy one column - to calculate
- // total height of options+parameters
- fl = new FlowLayout(FlowLayout.LEFT);
- // helpful hint from
- // http://stackoverflow.com/questions/2743177/top-alignment-for-flowlayout
- fl.setAlignOnBaseline(true);
if (opanp.getParamSet().size() > 0)
{
- paramList.removeAll();
- paramList.setLayout(new MigLayout("", "", ""));
- fh = true;
+ paramsPanel.removeAll();
+ paramsPanel.setLayout(new MigLayout("", "", ""));
+ int hgap = 5;
+ int currentWidth = hgap;
+
+ JPanel lastAdded = null;
for (ParamBox pbox : opanp.getParamSet().values())
{
pbox.validate();
- cw += pbox.getSize().width + hgap;
- if (cw + 160 > panewidth)
+ int boxWidth = pbox.getSize().width;
+ currentWidth += boxWidth + hgap;
+ boolean wrapAfterLast = currentWidth > availableWidth
+ && lastAdded != null;
+ if (wrapAfterLast)
{
- paramList.add(pbox, "wrap");
- cw = pbox.getSize().width + hgap;
- fh = true;
+ paramsPanel.remove(lastAdded);
+ paramsPanel.add(lastAdded, "wrap");
+ currentWidth = pbox.getSize().width + hgap;
}
- else
- {
- paramList.add(pbox);
- }
- if (fh)
- {
- finalh += pbox.getSize().height + fl.getVgap();
- fh = false;
- }
-
+ paramsPanel.add(pbox);
+ lastAdded = pbox;
}
+
/*
* s = 2 * sep; for (ParamBox pbox : opanp.getParamSet().values()) {
* pbox.validate(); s += sep +
* .getBorder().getBorderInsets(paramList).bottom+paramList
* .getBorder().getBorderInsets(paramList).top;
*/
- paramList.revalidate();
+ paramsPanel.revalidate();
}
else
{
- paramList.setVisible(false);
+ paramsPanel.setVisible(false);
}
// TODO: waste some time trying to eliminate any unnecessary .validate calls
// here
paramPane.revalidate();
revalidate();
}
-
- /**
- * testing method - grab a service and parameter set and show the window
- *
- * @param args
- * @j2sIgnore
- */
- public static void main(String[] args)
- {
- jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
- .getInstance();
- int p = 0;
- if (args.length > 0)
- {
- Vector<String> services = new Vector<>();
- services.addElement(args[p++]);
- Jws2Discoverer.getInstance().setServiceUrls(services);
- }
- try
- {
- disc.run();
- } catch (Exception e)
- {
- System.err.println("Aborting. Problem discovering services.");
- e.printStackTrace();
- return;
- }
- Jws2Instance lastserv = null;
- for (Jws2Instance service : disc.getServices())
- {
- lastserv = service;
- if (p >= args.length || service.serviceType.equalsIgnoreCase(args[p]))
- {
- if (lastserv != null)
- {
- List<Preset> prl = null;
- Preset pr = null;
- if (++p < args.length)
- {
- PresetManager prman = lastserv.getPresets();
- if (prman != null)
- {
- pr = prman.getPresetByName(args[p]);
- if (pr == null)
- {
- // just grab the last preset.
- prl = prman.getPresets();
- }
- }
- }
- else
- {
- PresetManager prman = lastserv.getPresets();
- if (prman != null)
- {
- prl = prman.getPresets();
- }
- }
- Iterator<Preset> en = (prl == null) ? null : prl.iterator();
- while (en != null && en.hasNext())
- {
- if (en != null)
- {
- if (!en.hasNext())
- {
- en = prl.iterator();
- }
- pr = en.next();
- }
- {
- System.out.println("Testing opts dupes for "
- + lastserv.getUri() + " : " + lastserv.getActionText()
- + ":" + pr.getName());
- List<Option> rg = lastserv.getRunnerConfig().getOptions();
- for (Option o : rg)
- {
- try
- {
- Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
- } catch (Exception e)
- {
- System.err.println("Failed to copy " + o.getName());
- e.printStackTrace();
- } catch (Error e)
- {
- System.err.println("Failed to copy " + o.getName());
- e.printStackTrace();
- }
- }
- }
- {
- System.out.println("Testing param dupes:");
- List<Parameter> rg = lastserv.getRunnerConfig()
- .getParameters();
- for (Parameter o : rg)
- {
- try
- {
- Parameter cpy = jalview.ws.jws2.ParameterUtils
- .copyParameter(o);
- } catch (Exception e)
- {
- System.err.println("Failed to copy " + o.getName());
- e.printStackTrace();
- } catch (Error e)
- {
- System.err.println("Failed to copy " + o.getName());
- e.printStackTrace();
- }
- }
- }
- {
- System.out.println("Testing param write:");
- List<String> writeparam = null, readparam = null;
- try
- {
- writeparam = jalview.ws.jws2.ParameterUtils
- .writeParameterSet(
- pr.getArguments(lastserv.getRunnerConfig()),
- " ");
- System.out.println("Testing param read :");
- List<Option> pset = jalview.ws.jws2.ParameterUtils
- .processParameters(writeparam,
- lastserv.getRunnerConfig(), " ");
- readparam = jalview.ws.jws2.ParameterUtils
- .writeParameterSet(pset, " ");
- Iterator<String> o = pr.getOptions().iterator(),
- s = writeparam.iterator(), t = readparam.iterator();
- boolean failed = false;
- while (s.hasNext() && t.hasNext())
- {
- String on = o.next(), sn = s.next(), st = t.next();
- if (!sn.equals(st))
- {
- System.out.println(
- "Original was " + on + " Phase 1 wrote " + sn
- + "\tPhase 2 wrote " + st);
- failed = true;
- }
- }
- if (failed)
- {
- System.out.println(
- "Original parameters:\n" + pr.getOptions());
- System.out.println(
- "Wrote parameters in first set:\n" + writeparam);
- System.out.println(
- "Wrote parameters in second set:\n" + readparam);
-
- }
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- }
- WsJobParameters pgui = new WsJobParameters(lastserv,
- new JabaPreset(lastserv, pr));
- JFrame jf = new JFrame(MessageManager
- .formatMessage("label.ws_parameters_for", new String[]
- { lastserv.getActionText() }));
- JPanel cont = new JPanel(new BorderLayout());
- pgui.validate();
- cont.setPreferredSize(pgui.getPreferredSize());
- cont.add(pgui, BorderLayout.CENTER);
- jf.setLayout(new BorderLayout());
- jf.add(cont, BorderLayout.CENTER);
- jf.validate();
- final Thread thr = Thread.currentThread();
- jf.addWindowListener(new WindowListener()
- {
-
- @Override
- public void windowActivated(WindowEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void windowClosed(WindowEvent e)
- {
- }
-
- @Override
- public void windowClosing(WindowEvent e)
- {
- thr.interrupt();
-
- }
-
- @Override
- public void windowDeactivated(WindowEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void windowDeiconified(WindowEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void windowIconified(WindowEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void windowOpened(WindowEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- });
- jf.setVisible(true);
- boolean inter = false;
- while (!inter)
- {
- try
- {
- Thread.sleep(10000);
- } catch (Exception e)
- {
- inter = true;
- }
- }
- jf.dispose();
- }
- }
- }
- }
- }
-
public boolean isServiceDefaults()
{
return (!isModified()
return opanp.getCurrentSettings();
}
- String lastParmSet = null;
-
/*
* Hashtable<String, Object[]> editedParams = new Hashtable<String,
* Object[]>();
int n = 0;
// remove any set names in the drop down menu that aren't either a reserved
// setting, or a user defined or service preset.
- Vector items = new Vector();
+ Vector<String> items = new Vector<>();
while (n < setName.getItemCount())
{
- String item = (String) setName.getItemAt(n);
+ String item = setName.getItemAt(n);
if (!item.equals(SVC_DEF) && !paramStore.presetExists(item))
{
setName.removeItemAt(n);
initArgSetModified();
syncSetNamesWithStore();
setName.setSelectedItem(lastParmSet);
- SetNamePanel.validate();
+ setNamePanel.validate();
validate();
settingDialog = false;
}
*/
protected void updateWebServiceMenus()
{
- if (Desktop.instance == null)
++ if (Desktop.getInstance() == null)
+ {
+ return;
+ }
for (AlignFrame alignFrame : Desktop.getAlignFrames())
{
- alignFrame.BuildWebServiceMenu();
+ alignFrame.buildWebServicesMenu();
}
}
@Override
public void itemStateChanged(ItemEvent e)
{
- if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
+ if (e.getSource() == setName
+ && e.getStateChange() == ItemEvent.SELECTED)
{
final String setname = (String) setName.getSelectedItem();
- System.out.println("Item state changed for " + setname
- + " (handling ? " + !settingDialog + ")");
+ // System.out.println("Item state changed for " + setname
+ // + " (handling ? " + !settingDialog + ")");
if (settingDialog)
{
// ignore event
}
- private void _renameExistingPreset(String oldName, String curSetName2)
- {
- paramStore.updatePreset(oldName, curSetName2, setDescr.getText(),
- getJobParams());
- }
-
/**
* store current settings as given name. You should then reset gui.
*
*/
public class WsParamSetManager implements ParamManager
{
+ private static final String WS_PARAM_FILES = "WS_PARAM_FILES";
Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<>();
@Override
public WsParamSetI[] getParameterSet(String name, String serviceUrl,
boolean modifiable, boolean unmodifiable)
{
- String files = Cache.getProperty("WS_PARAM_FILES");
+ String files = Cache.getProperty(WS_PARAM_FILES);
if (files == null)
{
return null;
} catch (IOException e)
{
Cache.log.info("Failed to parse parameter file " + pfile
- + " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
+ + " (Check that all " + WS_PARAM_FILES
+ + " entries are valid!)",
e);
}
}
chooser.setDialogTitle(MessageManager
.getString("label.choose_filename_for_param_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
- int value = chooser.showSaveDialog(Desktop.instance);
+ int value = chooser.showSaveDialog(Desktop.getInstance());
if (value == JalviewFileChooser.APPROVE_OPTION)
{
outfile = chooser.getSelectedFile();
}
if (outfile != null)
{
- String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES",
+ String paramFiles = jalview.bin.Cache.getDefault(WS_PARAM_FILES,
filename);
if (paramFiles.indexOf(filename) == -1)
{
}
paramFiles = paramFiles.concat(filename);
}
- Cache.setProperty("WS_PARAM_FILES", paramFiles);
+
+ Cache.setProperty(WS_PARAM_FILES, paramFiles);
WebServiceParameterSet paramxml = new WebServiceParameterSet();
{
return;
}
- String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES", "");
+ String paramFiles = jalview.bin.Cache.getDefault(WS_PARAM_FILES, "");
if (paramFiles.indexOf(filename) > -1)
{
String nparamFiles = new String();
nparamFiles = nparamFiles.concat("|").concat(fl);
}
}
- jalview.bin.Cache.setProperty("WS_PARAM_FILES", nparamFiles);
+ jalview.bin.Cache.setProperty(WS_PARAM_FILES, nparamFiles);
}
try
File pfile = new File(filename);
if (pfile.exists() && pfile.canWrite())
{
- if (JvOptionPane.showConfirmDialog(Desktop.instance,
+ if (JvOptionPane.showConfirmDialog(Desktop.getInstance(),
"Delete the preset's file, too ?", "Delete User Preset ?",
JvOptionPane.OK_CANCEL_OPTION) == JvOptionPane.OK_OPTION)
{
*/
package jalview.gui;
- import jalview.bin.Cache;
- import jalview.jbgui.GWsPreferences;
- import jalview.util.MessageManager;
- import jalview.ws.WSDiscovererI;
- import jalview.ws.jws2.Jws2Discoverer;
- import jalview.ws.rest.RestServiceDescription;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.net.URL;
+import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.TableCellRenderer;
+ import jalview.bin.Cache;
+ import jalview.jbgui.GWsPreferences;
+ import jalview.util.MessageManager;
++import jalview.ws.WSDiscovererI;
+ import jalview.ws.jws2.Jws2Discoverer;
+ import jalview.ws.rest.RestServiceDescription;
+
public class WsPreferences extends GWsPreferences
{
private void initFromPreferences()
{
- wsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
+ wsUrls = Jws2Discoverer.getInstance().getServiceUrls();
if (!wsUrls.isEmpty())
{
oldUrls = new Vector<String>(wsUrls);
int r = 0;
for (String url : wsUrls)
{
- int status = Jws2Discoverer.getDiscoverer().getServerStatusFor(url);
+ int status = Jws2Discoverer.getInstance().getServerStatusFor(url);
tdat[r][1] = Integer.valueOf(status);
tdat[r++][0] = url;
}
String t = new String("");
switch (((Integer) status).intValue())
{
- case 1:
+ case WSDiscovererI.STATUS_OK:
// cb.setSelected(true);
// cb.setBackground(
c = Color.green;
break;
- case 0:
+ case WSDiscovererI.STATUS_NO_SERVICES:
// cb.setSelected(true);
// cb.setBackground(
c = Color.lightGray;
break;
- case -1:
+ case WSDiscovererI.STATUS_INVALID:
// cb.setSelected(false);
// cb.setBackground(
c = Color.red;
break;
+ case WSDiscovererI.STATUS_UNKNOWN:
default:
// cb.setSelected(false);
// cb.setBackground(
private void updateServiceList()
{
- Jws2Discoverer.getDiscoverer().setServiceUrls(wsUrls);
+ Jws2Discoverer.getInstance().setServiceUrls(wsUrls);
}
private void updateRsbsServiceList()
boolean valid = false;
int resp = JvOptionPane.CANCEL_OPTION;
while (!valid && (resp = JvOptionPane.showInternalConfirmDialog(
- Desktop.desktop, panel, title,
+ Desktop.getDesktopPane(), panel, title,
JvOptionPane.OK_CANCEL_OPTION)) == JvOptionPane.OK_OPTION)
{
try
} catch (Exception e)
{
valid = false;
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.invalid_url"));
}
}
if (valid && resp == JvOptionPane.OK_OPTION)
{
- int validate = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int validate = JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(),
MessageManager.getString("info.validate_jabaws_server"),
MessageManager.getString("label.test_server"),
JvOptionPane.YES_NO_OPTION);
if (validate == JvOptionPane.OK_OPTION)
{
- if (Jws2Discoverer.getDiscoverer().testServiceUrl(foo))
- if (Jws2Discoverer.testServiceUrl(foo))
++ if (Jws2Discoverer.getInstance().testServiceUrl(foo))
{
return foo.toString();
}
else
{
- int opt = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+ int opt = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
"The Server '" + foo.toString()
+ "' failed validation,\ndo you want to add it anyway? ",
"Server Validation Failed", JvOptionPane.YES_NO_OPTION,
}
else
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString(
"warn.server_didnt_pass_validation"));
}
if (lastrefresh != update)
{
lastrefresh = update;
- Desktop.instance.startServiceDiscovery(true); // wait around for all
+ Desktop.getInstance().startServiceDiscovery(true); // wait around for all
// threads to complete
updateList();
public void run()
{
long ct = System.currentTimeMillis();
- Desktop.instance.setProgressBar(MessageManager
+ Desktop.getInstance().setProgressBar(MessageManager
.getString("status.refreshing_web_service_menus"), ct);
if (lastrefresh != update)
{
lastrefresh = update;
- Desktop.instance.startServiceDiscovery(true);
+ Desktop.getInstance().startServiceDiscovery(true);
updateList();
}
- Desktop.instance.setProgressBar(null, ct);
+ Desktop.getInstance().setProgressBar(null, ct);
}
}).start();
@Override
protected void resetWs_actionPerformed(ActionEvent e)
{
- Jws2Discoverer.getDiscoverer().setServiceUrls(null);
- List<String> nwsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
+ Jws2Discoverer.getInstance().setServiceUrls(null);
+ List<String> nwsUrls = Jws2Discoverer.getInstance().getServiceUrls();
if (!wsUrls.equals(nwsUrls))
{
update++;
--- /dev/null
+package jalview.io;
+
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ResidueCount;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import javax.swing.JFileChooser;
+
+public class CountReader
+{
+ public static ResidueCount getBackgroundFrequencies(AlignmentPanel ap, SequenceI seq) throws MalformedURLException, IOException
+ {
+ JFileChooser bkgdFreqChooser = new JFileChooser();
+
+ bkgdFreqChooser.showOpenDialog(ap);
+
+ File file = bkgdFreqChooser.getSelectedFile();
+ if (file == null)
+ {
+ return null;
+ }
+
+ IdentifyFile identifier = new IdentifyFile();
+ FileFormatI format = null;
+ try
+ {
+ format = identifier.identify(file.getPath(), DataSourceType.FILE);
+ } catch (Exception e)
+ {
+
+ }
+
+ if (format == null)
+ {
+ if (!Jalview.isHeadlessMode())
+ {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
++ JvOptionPane.showInternalMessageDialog(Desktop.getInstance(),
+ MessageManager.getString("label.couldnt_read_data") + " in "
+ + file + "\n"
+ + AppletFormatAdapter.getSupportedFormats(),
+ MessageManager.getString("label.couldnt_read_data"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ }
+
+ FileParse parser = new FileParse(file.getPath(), DataSourceType.FILE);
+ AlignmentI al = new FormatAdapter().readFromFile(parser, format);
+ parser.close();
+
+ ResidueCount counts = new ResidueCount(al.getSequences());
+
+ return counts;
+ }
+}
{
return true;
}
+ },
+ HMMER3("HMMER3", "hmm", true, true)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ return new HMMFile(source);
+ }
+
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ return new HMMFile();
+ }
+ }, BSML("BSML", "bbb", true, false)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ return new BSMLFile(source);
+ }
+
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ return null;
+ }
};
+
private boolean writable;
private boolean readable;
*/
package jalview.io;
+ import java.awt.Dimension;
import java.io.File;
import java.io.IOException;
import java.util.StringTokenizer;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+ import jalview.util.Platform;
import jalview.ws.utils.UrlDownloadClient;
+import java.util.ArrayList;
+import java.util.List;
+
public class FileLoader implements Runnable
{
+ private static final String TAB = "\t";
+
String file;
DataSourceType protocol;
return alignFrame;
}
- public void updateRecentlyOpened()
+ public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport,
+ String file, DataSourceType sourceType, FileFormatI format)
{
Vector<String> recent = new Vector<>();
if (protocol == DataSourceType.PASTE)
+ this.viewport = viewport;
+ this.file = file;
+ this.protocol = sourceType;
+ this.format = format;
+ _LoadFileWaitTillLoaded();
+ }
+
+
+ /**
+ * Updates (or creates) the tab-separated list of recently opened files held
+ * under the given property name by inserting the filePath at the front of the
+ * list. Duplicates are removed, and the list is limited to 11 entries. The
+ * method returns the updated value of the property.
+ *
+ * @param filePath
+ * @param sourceType
+ */
+ public static String updateRecentlyOpened(String filePath,
+ DataSourceType sourceType)
+ {
+ if (sourceType != DataSourceType.FILE
+ && sourceType != DataSourceType.URL)
{
- // do nothing if the file was pasted in as text... there is no filename to
- // refer to it as.
- return;
+ return null;
}
- if (file != null
- && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+
+ String propertyName = sourceType == DataSourceType.FILE ? "RECENT_FILE"
+ : "RECENT_URL";
+ String historyItems = Cache.getProperty(propertyName);
+ if (filePath != null
+ && filePath.indexOf(System.getProperty("java.io.tmpdir")) > -1)
{
// ignore files loaded from the system's temporary directory
- return;
+ return null;
}
- String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
- : "RECENT_URL";
- String historyItems = Cache.getProperty(type);
-
- StringTokenizer st;
+ List<String> recent = new ArrayList<>();
if (historyItems != null)
{
- st = new StringTokenizer(historyItems, "\t");
+ StringTokenizer st = new StringTokenizer(historyItems, TAB);
while (st.hasMoreTokens())
{
- recent.addElement(st.nextToken().trim());
+ String trimmed = st.nextToken().trim();
+ recent.add(trimmed);
}
}
- if (recent.contains(file))
+ /*
+ * if file was already in the list, it moves to the top
+ */
+ if (recent.contains(filePath))
{
- recent.remove(file);
+ recent.remove(filePath);
}
- StringBuffer newHistory = new StringBuffer(file);
+ StringBuilder newHistory = new StringBuilder(filePath);
for (int i = 0; i < recent.size() && i < 10; i++)
{
- newHistory.append("\t");
- newHistory.append(recent.elementAt(i));
+ newHistory.append(TAB);
+ newHistory.append(recent.get(i));
}
- Cache.setProperty(type, newHistory.toString());
+ String newProperty = newHistory.toString();
+ Cache.setProperty(propertyName, newProperty);
- if (protocol == DataSourceType.FILE)
- {
- Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
- }
+ return newProperty;
}
@Override
Runtime rt = Runtime.getRuntime();
try
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.startLoading(file);
+ Desktop.getInstance().startLoading(file);
}
if (format == null)
{
if (format == null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
System.err.println("The input file \"" + file
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.couldnt_read_data")
+ " in " + file + "\n"
+ AppletFormatAdapter.getSupportedFormats(),
}
// TODO: cache any stream datasources as a temporary file (eg. PDBs
// retrieved via URL)
- if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
{
System.gc();
memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
// register PDB entries with desktop's structure selection
// manager
StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Desktop.getInstance())
.registerPDBEntry(pdbe);
}
}
}
// append to existing alignment
viewport.addAlignment(al, title);
+ if (source instanceof HMMFile)
+ {
+ AlignmentI alignment = viewport.getAlignment();
+ SequenceI seq = alignment
+ .getSequenceAt(alignment.getHeight() - 1);
+ if (seq.hasHMMProfile())
+ {
+ /*
+ * fudge: move HMM consensus sequence from last to first
+ */
+ alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+ alignment.insertSequenceAt(0, seq);
+ }
+ viewport.getAlignPanel().adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ }
}
else
{
// add metadata and update ui
if (!(protocol == DataSourceType.PASTE))
{
- alignFrame.setFileName(file, format);
- alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
+ alignFrame.setFile(file, selectedFile, protocol, format);
}
if (proxyColourScheme != null)
{
// status in Jalview 3
// TODO: define 'virtual desktop' for benefit of headless scripts
// that perform queries to find the 'current working alignment'
- Desktop.addInternalFrame(alignFrame, title,
+
+ Dimension dim = Platform.getDimIfEmbedded(alignFrame,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ alignFrame.setSize(dim);
+ Desktop.addInternalFrame(alignFrame, title, dim.width,
+ dim.height);
}
try
}
else
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
final String errorMessage = MessageManager.getString(
"label.couldnt_load_file") + " " + title + "\n" + error;
// TODO: refactor FileLoader to be independent of Desktop / Applet GUI
// bits ?
- if (raiseGUI && Desktop.desktop != null)
+ if (raiseGUI && Desktop.getDesktopPane() != null)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
errorMessage,
MessageManager
.getString("label.error_loading_file"),
}
}
- updateRecentlyOpened();
+ updateRecentlyOpened(file, protocol);
+
+ if (protocol == DataSourceType.FILE && format != null)
+ {
+ Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
+ }
} catch (Exception er)
{
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.problems_opening_file", new String[]
{ file }),
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"warn.out_of_memory_loading_file", new String[]
{ file }),
// memory
// after
// load
- if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
{
if (alignFrame != null)
{
}
}
// remove the visual delay indicator
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
}
reply = FileFormat.ScoreMatrix;
break;
}
+ if (data.startsWith("HMMER3"))
+ {
+ reply = FileFormat.HMMER3;
+ break;
+ }
if (data.startsWith("H ") && !aaIndexHeaderRead)
{
aaIndexHeaderRead = true;
reply = FileFormat.Rnaml;
break;
}
+ if (upper.substring(lessThan).startsWith("<BSML"))
+ {
+ reply = FileFormat.BSML;
+ break;
+ }
}
if ((data.length() < 1) || (data.indexOf("#") == 0))
import java.util.Map;
import jalview.api.FeatureColourI;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.GeneLociI;
{
if (sb0.length() > 6)
{
- sb.append("<br/>");
+ sb.append("<br>");
}
sb.append(feature.getType()).append(" ").append(begin).append(":")
.append(end);
if (sb0.length() > 6)
{
- sb.append("<br/>");
+ sb.append("<br>");
}
// TODO: remove this hack to display link only features
boolean linkOnly = feature.getValue("linkonly") != null;
int linkindex = description.toLowerCase().indexOf("<a ");
boolean hasLink = linkindex > -1
&& linkindex < MAX_DESCRIPTION_LENGTH;
- if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
+ if (
+ // BH suggestion maxlength == 0 &&
+ description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
{
description = description.substring(0, MAX_DESCRIPTION_LENGTH)
+ ELLIPSIS;
{
for (List<String> urllink : createLinksFrom(null, urlstring))
{
- sb.append("<br/> <a href=\""
+ sb.append("<br> <a href=\""
+ urllink.get(3)
+ "\" target=\""
+ urllink.get(0)
.equals(urllink.get(1).toLowerCase()) ? urllink
.get(0) : (urllink.get(0) + ":" + urllink
.get(1)))
- + "</a><br/>");
+ + "</a><br>");
}
} catch (Exception x)
{
sb.append(tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
+
SequenceI ds = sequence;
while (ds.getDatasetSequence() != null)
{
ds = ds.getDatasetSequence();
}
+ /*
+ * add any annotation scores
+ */
+ AlignmentAnnotation[] anns = ds.getAnnotation();
+ for (int i = 0; anns != null && i < anns.length; i++)
+ {
+ AlignmentAnnotation aa = anns[i];
+ if (aa != null && aa.hasScore() && aa.sequenceRef != null)
+ {
+ sb.append("<br>").append(aa.label).append(": ")
+ .append(aa.getScore());
+ }
+ }
+
if (showDbRefs)
{
maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
maxWidth = Math.max(maxWidth, sz);
}
}
+
+
+ if (sequence.getAnnotation("Search Scores") != null)
+ {
+ sb.append("<br>");
+ String eValue = " E-Value: "
+ + sequence.getAnnotation("Search Scores")[0].getEValue();
+ String bitScore = " Bit Score: "
+ + sequence.getAnnotation("Search Scores")[0].getBitScore();
+ sb.append(eValue);
+ sb.append("<br>");
+ sb.append(bitScore);
+ maxWidth = Math.max(maxWidth, eValue.length());
+ maxWidth = Math.max(maxWidth, bitScore.length());
+ }
+ sb.append("<br>");
sb.append("</i>");
+
return maxWidth;
}
countForSource++;
if (countForSource == 1 || !summary)
{
- sb.append("<br/>");
+ sb.append("<br>");
}
if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
{
}
if (moreSources)
{
- sb.append("<br/>").append(source).append(COMMA).append(ELLIPSIS);
+ sb.append("<br>").append(source).append(COMMA).append(ELLIPSIS);
}
if (ellipsis)
{
- sb.append("<br/>(");
+ sb.append("<br>(");
sb.append(MessageManager.getString("label.output_seq_details"));
sb.append(")");
}
*/
package jalview.io;
+ import jalview.analysis.Rna;
+ import jalview.datamodel.AlignmentAnnotation;
+ import jalview.datamodel.AlignmentI;
+ import jalview.datamodel.Annotation;
+ import jalview.datamodel.DBRefEntry;
+ import jalview.datamodel.DBRefSource;
+ import jalview.datamodel.Mapping;
+ import jalview.datamodel.Sequence;
+ import jalview.datamodel.SequenceFeature;
+ import jalview.datamodel.SequenceI;
+ import jalview.schemes.ResidueProperties;
+ import jalview.util.Comparison;
+ import jalview.util.DBRefUtils;
+ import jalview.util.Format;
+ import jalview.util.MessageManager;
+ import jalview.util.Platform;
+
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import fr.orsay.lri.varna.factories.RNAFactory;
import fr.orsay.lri.varna.models.rna.RNA;
- import jalview.analysis.Rna;
- import jalview.datamodel.AlignmentAnnotation;
- import jalview.datamodel.AlignmentI;
- import jalview.datamodel.Annotation;
- import jalview.datamodel.DBRefEntry;
- import jalview.datamodel.DBRefSource;
- import jalview.datamodel.Mapping;
- import jalview.datamodel.Sequence;
- import jalview.datamodel.SequenceFeature;
- import jalview.datamodel.SequenceI;
- import jalview.schemes.ResidueProperties;
- import jalview.util.Comparison;
- import jalview.util.DBRefUtils;
- import jalview.util.Format;
- import jalview.util.MessageManager;
// import org.apache.log4j.*;
{
private static final String ANNOTATION = "annotation";
- // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using
- // NOT_RNASS first.
+ private static final char UNDERSCORE = '_';
+
+ // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first.
+
public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
+ public static final int REGEX_STOCKHOLM = 0;
+
+ public static final int REGEX_BRACKETS = 1;
+
// use the following regex to decide an annotations (whole) line is NOT an RNA
// SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
- private static final Regex NOT_RNASS = new Regex(
- "^[^<>[\\](){}A-DF-Za-df-z]*$");
+ public static final int REGEX_NOT_RNASS = 2;
+
+ private static final int REGEX_ANNOTATION = 3;
+
+ private static final int REGEX_PFAM = 4;
+
+ private static final int REGEX_RFAM = 5;
+
+ private static final int REGEX_ALIGN_END = 6;
+
+ private static final int REGEX_SPLIT_ID = 7;
+
+ private static final int REGEX_SUBTYPE = 8;
+
+ private static final int REGEX_ANNOTATION_LINE = 9;
+
+ private static final int REGEX_REMOVE_ID = 10;
+
+ private static final int REGEX_OPEN_PAREN = 11;
+
+ private static final int REGEX_CLOSE_PAREN = 12;
+
+ public static final int REGEX_MAX = 13;
+
+ private static Regex REGEX[] = new Regex[REGEX_MAX];
+
+ /**
+ * Centralize all actual Regex instantialization in Platform.
- *
++ * // JBPNote: Why is this 'centralisation' better ?
+ * @param id
+ * @return
+ */
+ private static Regex getRegex(int id)
+ {
+ if (REGEX[id] == null)
+ {
+ String pat = null, pat2 = null;
+ switch (id)
+ {
+ case REGEX_STOCKHOLM:
+ pat = "# STOCKHOLM ([\\d\\.]+)";
+ break;
+ case REGEX_BRACKETS:
+ // for reference; not used
+ pat = "(<|>|\\[|\\]|\\(|\\)|\\{|\\})";
+ break;
+ case REGEX_NOT_RNASS:
+ pat = "^[^<>[\\](){}A-DF-Za-df-z]*$";
+ break;
+ case REGEX_ANNOTATION:
+ pat = "(\\w+)\\s*(.*)";
+ break;
+ case REGEX_PFAM:
+ pat = "PF[0-9]{5}(.*)";
+ break;
+ case REGEX_RFAM:
+ pat = "RF[0-9]{5}(.*)";
+ break;
+ case REGEX_ALIGN_END:
+ pat = "^\\s*\\/\\/";
+ break;
+ case REGEX_SPLIT_ID:
+ pat = "(\\S+)\\/(\\d+)\\-(\\d+)";
+ break;
+ case REGEX_SUBTYPE:
+ pat = "(\\S+)\\s+(\\S*)\\s+(.*)";
+ break;
+ case REGEX_ANNOTATION_LINE:
+ pat = "#=(G[FSRC]?)\\s+(.*)";
+ break;
+ case REGEX_REMOVE_ID:
+ pat = "(\\S+)\\s+(\\S+)";
+ break;
+ case REGEX_OPEN_PAREN:
+ pat = "(<|\\[)";
+ pat2 = "(";
+ break;
+ case REGEX_CLOSE_PAREN:
+ pat = "(>|\\])";
+ pat2 = ")";
+ break;
+ default:
+ return null;
+ }
+ REGEX[id] = Platform.newRegex(pat, pat2);
+ }
+ return REGEX[id];
+ }
StringBuffer out; // output buffer
- AlignmentI al;
+ private AlignmentI al;
public StockholmFile()
{
}
/**
- * Creates a new StockholmFile object for output.
+ * Creates a new StockholmFile object for output
*/
public StockholmFile(AlignmentI al)
{
// First, we have to check that this file has STOCKHOLM format, i.e. the
// first line must match
- r = new Regex("# STOCKHOLM ([\\d\\.]+)");
+ r = getRegex(REGEX_STOCKHOLM);
if (!r.search(nextLine()))
{
throw new IOException(MessageManager
// logger.debug("Stockholm version: " + version);
}
- // We define some Regexes here that will be used regularly later
- rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
- p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
+ // We define some Regexes here that will be used regularily later
+ rend = getRegex(REGEX_ALIGN_END);//"^\\s*\\/\\/"); // Find the end of an alignment
+ p = getRegex(REGEX_SPLIT_ID);//"(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
// id/from/to
- s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
- r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
- x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
+ s = getRegex(REGEX_SUBTYPE);// "(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses
+ // annotation subtype
+ r = getRegex(REGEX_ANNOTATION_LINE);// "#=(G[FSRC]?)\\s+(.*)"); // Finds any
+ // annotation line
+ x = getRegex(REGEX_REMOVE_ID);// "(\\S+)\\s+(\\S+)"); // split id from
+ // sequence
// Convert all bracket types to parentheses (necessary for passing to VARNA)
- Regex openparen = new Regex("(<|\\[)", "(");
- Regex closeparen = new Regex("(>|\\])", ")");
+ Regex openparen = getRegex(REGEX_OPEN_PAREN);//"(<|\\[)", "(");
+ Regex closeparen = getRegex(REGEX_CLOSE_PAREN);//"(>|\\])", ")");
// // Detect if file is RNA by looking for bracket types
- // Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+ // Regex detectbrackets = getRegex("(<|>|\\[|\\]|\\(|\\))");
rend.optimize();
p.optimize();
this.noSeqs = seqs.size();
String dbsource = null;
- Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam
- Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam
+ Regex pf = getRegex(REGEX_PFAM); // Finds AC for Pfam
+ Regex rf = getRegex(REGEX_RFAM); // Finds AC for Rfam
if (getAlignmentProperty("AC") != null)
{
String dbType = getAlignmentProperty("AC").toString();
if (accAnnotations != null && accAnnotations.containsKey("AC"))
{
- String dbr = (String) accAnnotations.get("AC");
- if (dbr != null)
- {
- // we could get very clever here - but for now - just try to
+ String dbr = (String) accAnnotations.get("AC");
+ if (dbr != null)
+ {
+ // we could get very clever here - but for now - just try to
// guess accession type from type of sequence, source of alignment plus
// structure
- // of accession
- guessDatabaseFor(seqO, dbr, dbsource);
+ // of accession
+ guessDatabaseFor(seqO, dbr, dbsource);
}
// else - do what ? add the data anyway and prompt the user to
// specify what references these are ?
*/
// Let's save the annotations, maybe we'll be able to do something
// with them later...
- Regex an = new Regex("(\\w+)\\s*(.*)");
+ Regex an = getRegex(REGEX_ANNOTATION);
if (an.search(annContent))
{
if (an.stringMatched(1).equals("NH"))
if (features.containsKey(this.id2type(type)))
{
// logger.debug("Found content for " + this.id2type(type));
- content = (Hashtable) features.get(this.id2type(type));
+ content = (Hashtable) features
+ .get(this.id2type(type));
}
else
{
// logger.debug("Creating new content holder for " +
// this.id2type(type));
content = new Hashtable();
- features.put(this.id2type(type), content);
+ features.put(id2type(type), content);
}
String ns = (String) content.get(ANNOTATION);
Vector<AlignmentAnnotation> annotation, String label,
String annots)
{
- String convert1, convert2 = null;
-
- // convert1 = OPEN_PAREN.replaceAll(annots);
- // convert2 = CLOSE_PAREN.replaceAll(convert1);
+ String convert1, convert2 = null;
+ // String convert1 = OPEN_PAREN.replaceAll(annots);
+ // String convert2 = CLOSE_PAREN.replaceAll(convert1);
// annots = convert2;
String type = label;
type = id2type(type);
boolean isrnass = false;
+
if (type.equalsIgnoreCase("secondary structure"))
{
ss = true;
- isrnass = !NOT_RNASS.search(annots); // sorry about the double negative
+ isrnass = !getRegex(REGEX_NOT_RNASS).search(annots); // sorry about the double
+ // negative
// here (it's easier for dealing with
// other non-alpha-non-brace chars)
}
for (int i = 0; i < annots.length(); i++)
{
String pos = annots.substring(i, i + 1);
+ if (UNDERSCORE == pos.charAt(0))
+ {
+ pos = " ";
+ }
Annotation ann;
ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
// be written out
return ref.getSource().toString() + " ; "
+ ref.getAccessionId().toString();
}
+
@Override
public String print(SequenceI[] s, boolean jvSuffix)
{
}
else
{
- for (int idb = 0; idb < seq.getDBRefs().size(); idb++)
+ for (int idb = 0; idb < ndb; idb++)
{
- DBRefEntry dbref = seq.getDBRefs().get(idb);
+ DBRefEntry dbref = seqrefs.get(idb);
dataRef.put(tmp, dbref_to_ac_record(dbref));
// if we put in a uniprot or EMBL record then we're done:
- if (isAA && DBRefSource.UNIPROT
- .equals(DBRefUtils.getCanonicalName(dbref.getSource())))
- {
- break;
- }
- if (!isAA && DBRefSource.EMBL
+ if ((isAA ? DBRefSource.UNIPROT : DBRefSource.EMBL)
.equals(DBRefUtils.getCanonicalName(dbref.getSource())))
{
break;
if (alAnot != null)
{
Annotation[] ann;
- for (int j = 0, nj = alAnot.length; j < nj; j++)
+ for (int j = 0; j < alAnot.length; j++)
{
-
- String key = type2id(alAnot[j].label);
- boolean isrna = alAnot[j].isValidStruc();
-
- if (isrna)
- {
- // hardwire to secondary structure if there is RNA secondary
- // structure on the annotation
- key = "SS";
- }
- if (key == null)
+ if (alAnot[j].annotations != null)
{
+ String key = type2id(alAnot[j].label);
+ boolean isrna = alAnot[j].isValidStruc();
- continue;
- }
+ if (isrna)
+ {
+ // hardwire to secondary structure if there is RNA secondary
+ // structure on the annotation
+ key = "SS";
+ }
+ if (key == null)
+ {
+ continue;
+ }
- // out.append("#=GR ");
- out.append(new Format("%-" + maxid + "s").form(
- "#=GR " + printId(seq, jvSuffix) + " " + key + " "));
- ann = alAnot[j].annotations;
- String sseq = "";
- for (int k = 0, nk = ann.length; k < nk; k++)
- {
- sseq += outputCharacter(key, k, isrna, ann, seq);
- }
- out.append(sseq);
- out.append(newline);
+ // out.append("#=GR ");
+ out.append(new Format("%-" + maxid + "s").form(
+ "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
+ ann = alAnot[j].annotations;
+ String sseq = "";
+ for (int k = 0; k < ann.length; k++)
+ {
+ sseq += outputCharacter(key, k, isrna, ann, s[i]);
+ }
+ out.append(sseq);
+ out.append(newline);
+ }
}
+
}
out.append(new Format("%-" + maxid + "s")
return out.toString();
}
+
/**
* add an annotation character to the output row
*
: seq;
}
+ /**
+ * make a friendly ID string.
+ *
+ * @param dataName
+ * @return truncated dataName to after last '/'
+ */
+ private String safeName(String dataName)
+ {
+ int b = 0;
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+ {
+ dataName = dataName.substring(b + 1).trim();
+
+ }
+ int e = (dataName.length() - dataName.indexOf(".")) + 1;
+ dataName = dataName.substring(1, e).trim();
+ return dataName;
+ }
+
+
public String print()
{
out = new StringBuffer();
}
}
-
+
protected static String id2type(String id)
{
if (typeIds.containsKey(id))
"Warning : Unknown Stockholm annotation type: " + type);
return key;
}
-
- /**
- * make a friendly ID string.
- *
- * @param dataName
- * @return truncated dataName to after last '/'
- */
- private String safeName(String dataName)
- {
- int b = 0;
- while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
- {
- dataName = dataName.substring(b + 1).trim();
-
- }
- int e = (dataName.length() - dataName.indexOf(".")) + 1;
- dataName = dataName.substring(1, e).trim();
- return dataName;
- }
}
*/
package jalview.jbgui;
- import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
- import jalview.analysis.GeneticCodeI;
- import jalview.analysis.GeneticCodes;
- import jalview.api.SplitContainerI;
- import jalview.bin.Cache;
- import jalview.gui.JvSwingUtils;
- import jalview.gui.Preferences;
- import jalview.hmmer.HmmerCommand;
- import jalview.io.FileFormatException;
- import jalview.io.FileFormats;
- import jalview.schemes.ResidueColourScheme;
- import jalview.util.MessageManager;
- import jalview.util.Platform;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.GridLayout;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import java.awt.event.FocusEvent;
+ import java.awt.event.InputEvent;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+ import jalview.analysis.GeneticCodeI;
+ import jalview.analysis.GeneticCodes;
+ import jalview.api.SplitContainerI;
+ import jalview.bin.Cache;
+ import jalview.gui.JvSwingUtils;
+ import jalview.gui.Preferences;
++import jalview.hmmer.HmmerCommand;
++import jalview.io.FileFormatException;
+ import jalview.io.FileFormats;
+ import jalview.schemes.ResidueColourScheme;
+ import jalview.util.MessageManager;
+ import jalview.util.Platform;
+
++
@SuppressWarnings("serial")
public class GAlignFrame extends JInternalFrame
{
public JMenu webService = new JMenu();// BH 2019 was protected, but not
// sufficient for AlignFrame thread run
+ // JBP - followed suite for these other service related GUI elements.
+ // TODO: check we really need these to be public
+ public JMenu hmmerMenu = new JMenu();
- public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
- // sufficient for AlignFrame thread run
+ public JMenuItem webServiceNoServices;
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
protected JMenuItem openFeatureSettings;
{
// for Web-page embedding using id=align-frame-div
- setName("jalview-alignment");
+ setName(Platform.getAppID("alignment"));
+
jbInit();
setJMenuBar(alignFrameMenuBar);
private void jbInit() throws Exception
{
initColourMenu();
-
+
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
ActionListener al = new ActionListener()
saveAs_actionPerformed();
}
};
-
+
// FIXME getDefaultToolkit throws an exception in Headless mode
- KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Platform.SHORTCUT_KEY_MASK | InputEvent.SHIFT_DOWN_MASK,
false);
addMenuActionAndAccelerator(keyStroke, saveAs, al);
-
+
closeMenuItem.setText(MessageManager.getString("action.close"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
-
+
JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
JMenu annotationsMenu = new JMenu(
JMenu calculateMenu = new JMenu(
MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
+
+ initHMMERMenu();
+
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
-
+
JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.deselect_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
-
+
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
-
+
JMenuItem grpsFromSelection = new JMenuItem(
MessageManager.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(new ActionListener()
JMenuItem remove2LeftMenuItem = new JMenuItem(
MessageManager.getString("action.remove_left"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
-
+
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
-
+
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
-
+
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
}
};
addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
-
+
JMenuItem justifyLeftMenuItem = new JMenuItem(
MessageManager.getString("action.left_justify_alignment"));
justifyLeftMenuItem.addActionListener(new ActionListener()
sortGroupMenuItem_actionPerformed(e);
}
});
-
+ JMenuItem sortEValueMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_evalue"));
+ sortEValueMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortEValueMenuItem_actionPerformed(e);
+ }
+ });
+ JMenuItem sortBitScoreMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_bit_score"));
+ sortBitScoreMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortBitScoreMenuItem_actionPerformed(e);
+ }
+ });
+
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
};
addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
+ JMenuItem filterByEValue = new JMenuItem(
+ MessageManager.getString("action.filter_by_evalue"));
+ filterByEValue.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterByEValue_actionPerformed();
+ }
+
+ });
+
+ JMenuItem filterByScore = new JMenuItem(
+ MessageManager.getString("action.filter_by_score"));
+ filterByScore.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterByScore_actionPerformed();
+ }
+
+ });
+
JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
MessageManager.getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
-
+
this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
+
outputTextboxMenu
.setText(MessageManager.getString("label.out_to_textbox"));
+
annotationPanelMenuItem.setActionCommand("");
annotationPanelMenuItem
.setText(MessageManager.getString("label.show_annotations"));
final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
MessageManager.getString("label.sort_annotations_by_label"));
+
sortAnnBySequence.setSelected(
sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
sortAnnBySequence.addActionListener(new ActionListener()
colourTextMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem htmlMenuItem = new JMenuItem(
MessageManager.getString("label.html"));
htmlMenuItem.addActionListener(new ActionListener()
htmlMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem createBioJS = new JMenuItem(
MessageManager.getString("label.biojs_html_export"));
createBioJS.addActionListener(new java.awt.event.ActionListener()
bioJSMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem overviewMenuItem = new JMenuItem(
MessageManager.getString("label.overview_window"));
overviewMenuItem.addActionListener(new ActionListener()
overviewMenuItem_actionPerformed(e);
}
});
-
+
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
-
+
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
-
+
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new ActionListener()
{
wrapMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
-
+
renderGapsMenuItem
.setText(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.find_tip")));
al = new ActionListener()
showSeqFeatures.setText(
MessageManager.getString("label.show_sequence_features"));
+
showSeqFeatures.addActionListener(new ActionListener()
{
@Override
.setText(MessageManager.getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showDbRefs_actionPerformed(e);
}
-
+
});
showNpFeatsMenuitem.setText(
MessageManager.getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showNpFeats_actionPerformed(e);
}
-
+
});
showGroupConservation
.setText(MessageManager.getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showGroupConservation_actionPerformed(e);
}
-
+
});
showGroupConsensus
.setText(MessageManager.getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showGroupConsensus_actionPerformed(e);
}
-
+
});
showConsensusHistogram.setText(
MessageManager.getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showConsensusHistogram_actionPerformed(e);
}
-
+
});
showSequenceLogo
.setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showSequenceLogo_actionPerformed(e);
}
-
+
});
normaliseSequenceLogo
.setText(MessageManager.getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
normaliseSequenceLogo_actionPerformed(e);
}
-
+
});
applyAutoAnnotationSettings
.setText(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings_actionPerformed(e);
}
});
-
+
ButtonGroup buttonGroup = new ButtonGroup();
final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
MessageManager.getString("label.show_first"));
sortAnnotations_actionPerformed();
}
});
-
+
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
-
+
JMenuItem annotationColumn = new JMenuItem(
MessageManager.getString("action.select_by_annotation"));
annotationColumn.addActionListener(new ActionListener()
annotationColumn_actionPerformed(e);
}
});
-
+
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, createGroup, al);
-
+
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
}
};
addMenuActionAndAccelerator(keyStroke, unGroup, al);
-
+
copy.setText(MessageManager.getString("action.copy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
}
};
addMenuActionAndAccelerator(keyStroke, copy, al);
-
+
cut.setText(MessageManager.getString("action.cut"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, cut, al);
-
+
JMenuItem delete = new JMenuItem(
MessageManager.getString("action.delete"));
delete.addActionListener(new ActionListener()
delete_actionPerformed();
}
});
-
+
pasteMenu.setText(MessageManager.getString("action.paste"));
JMenuItem pasteNew = new JMenuItem(
MessageManager.getString("label.to_new_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- pasteNew_actionPerformed(e);
+ try
+ {
+ pasteNew_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
};
addMenuActionAndAccelerator(keyStroke, pasteNew, al);
-
+
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- pasteThis_actionPerformed(e);
+ try
+ {
+ pasteThis_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
};
addMenuActionAndAccelerator(keyStroke, pasteThis, al);
-
+
JMenuItem createPNG = new JMenuItem("PNG");
createPNG.addActionListener(new ActionListener()
{
});
createPNG.setActionCommand(
MessageManager.getString("label.save_png_image"));
-
JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
font.addActionListener(new ActionListener()
{
createEPS(null);
}
});
-
+
JMenuItem createSVG = new JMenuItem("SVG");
createSVG.addActionListener(new ActionListener()
{
createSVG(null);
}
});
-
+
JMenuItem loadTreeMenuItem = new JMenuItem(
MessageManager.getString("label.load_associated_tree"));
loadTreeMenuItem.setActionCommand(
loadTreeMenuItem_actionPerformed(e);
}
});
-
+
scaleAbove.setVisible(false);
scaleAbove.setText(MessageManager.getString("action.scale_above"));
scaleAbove.addActionListener(new ActionListener()
.setText(MessageManager.getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
followHighlight_actionPerformed();
}
-
+
});
-
+
sortByTreeMenu
.setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
@Override
public void menuSelected(MenuEvent e)
{
+ enableSortMenuOptions();
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+ });
+ sortByTreeMenu.addMenuListener(new MenuListener()
+ {
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
buildTreeSortMenu();
}
-
+
@Override
public void menuDeselected(MenuEvent e)
{
}
-
+
@Override
public void menuCanceled(MenuEvent e)
{
sort.add(sortByAnnotScore);
sort.addMenuListener(new javax.swing.event.MenuListener()
{
-
+
@Override
public void menuCanceled(MenuEvent e)
{
}
-
+
@Override
public void menuDeselected(MenuEvent e)
{
}
-
+
@Override
public void menuSelected(MenuEvent e)
{
showReverse_actionPerformed(true);
}
});
-
+
JMenuItem extractScores = new JMenuItem(
MessageManager.getString("label.extract_scores"));
extractScores.addActionListener(new ActionListener()
});
extractScores.setVisible(true);
// JBPNote: TODO: make gui for regex based score extraction
-
+
// for show products actions see AlignFrame.canShowProducts
showProducts.setText(MessageManager.getString("label.get_cross_refs"));
-
+
runGroovy.setText(MessageManager.getString("label.run_groovy"));
runGroovy.setToolTipText(
MessageManager.getString("label.run_groovy_tip"));
fetchSequence_actionPerformed();
}
});
-
+
JMenuItem associatedData = new JMenuItem(
MessageManager.getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- associatedData_actionPerformed(e);
+ try
+ {
+ associatedData_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
});
loadVcf = new JMenuItem(
listenToViewSelections_actionPerformed(e);
}
});
-
+
JMenu addSequenceMenu = new JMenu(
MessageManager.getString("label.add_sequences"));
JMenuItem addFromFile = new JMenuItem(
hiddenMarkers_actionPerformed(e);
}
});
-
+
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
- | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.ALT_DOWN_MASK,
false);
al = new ActionListener()
{
}
};
addMenuActionAndAccelerator(keyStroke, invertColSel, al);
-
+
showComplementMenuItem.setVisible(false);
showComplementMenuItem.addActionListener(new ActionListener()
{
showComplement_actionPerformed(showComplementMenuItem.getState());
}
});
-
+
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
{
@Override
tabbedPane_mousePressed(e);
}
}
-
+
@Override
public void mouseReleased(MouseEvent e)
{
tabbedPane_focusGained(e);
}
});
-
+
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, save, al);
-
+
reload.setEnabled(false);
reload.setText(MessageManager.getString("action.reload"));
reload.addActionListener(new ActionListener()
reload_actionPerformed(e);
}
});
-
+
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ Platform.SHORTCUT_KEY_MASK, false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, newView, al);
-
+
tabbedPane.setToolTipText("<html><i>"
+ MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ "</i></html>");
-
+
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
idRightAlign_actionPerformed(e);
}
});
-
+
gatherViews.setEnabled(false);
gatherViews.setText(MessageManager.getString("action.gather_views"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, gatherViews, al);
-
+
expandViews.setEnabled(false);
expandViews.setText(MessageManager.getString("action.expand_views"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, expandViews, al);
-
+
JMenuItem pageSetup = new JMenuItem(
MessageManager.getString("action.page_setup"));
pageSetup.addActionListener(new ActionListener()
});
JMenuItem selectHighlighted = new JMenuItem(
MessageManager.getString("action.select_highlighted_columns"));
- selectHighlighted.setToolTipText(
- MessageManager.getString("tooltip.select_highlighted_columns"));
+ selectHighlighted.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("tooltip.select_highlighted_columns")));
al = new ActionListener()
{
@Override
selectHighlightedColumns_actionPerformed(actionEvent);
}
};
+ JMenuItem Filter = new JMenuItem(
+ MessageManager.getString("action.select_highlighted_columns"));
+ selectHighlighted.setToolTipText(
+ MessageManager.getString("tooltip.select_highlighted_columns"));
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ selectHighlightedColumns_actionPerformed(actionEvent);
+ }
+ };
selectHighlighted.addActionListener(al);
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
JMenu autoAnnMenu = new JMenu(
MessageManager.getString("label.autocalculated_annotation"));
-
+
JMenu exportImageMenu = new JMenu(
MessageManager.getString("label.export_image"));
JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
+ alignFrameMenuBar.add(webService);
if (!Platform.isJS())
{
- alignFrameMenuBar.add(webService);
+ alignFrameMenuBar.add(hmmerMenu);
}
-
+
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
fileMenu.add(reload);
}
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
-
+
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
editMenu.add(undoMenuItem);
// editMenu.add(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
-
+ editMenu.addSeparator();
+ editMenu.add(filterByEValue);
+ editMenu.add(filterByScore);
+
showMenu.add(showAllColumns);
showMenu.add(showAllSeqs);
showMenu.add(showAllhidden);
viewMenu.add(alignmentProperties);
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
-
+
annotationsMenu.add(annotationPanelMenuItem);
annotationsMenu.addSeparator();
annotationsMenu.add(showAllAlAnnotations);
sort.add(sortLengthMenuItem);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
+ sort.add(sortEValueMenuItem);
+ sort.add(sortBitScoreMenuItem);
sort.add(sortByTreeMenu);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
calculateMenu.add(runGroovy);
}
-
webServiceNoServices = new JMenuItem(
MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
statusPanel.add(statusBar, null);
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
-
+
formatMenu.add(font);
formatMenu.addSeparator();
formatMenu.add(wrapMenuItem);
// selectMenu.add(listenToViewSelections);
}
+ /**
+ * Constructs the entries on the HMMER menu
+ */
+ protected void initHMMERMenu()
+ {
+ /*
+ * hmmbuild
+ */
+ JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
+ JMenuItem hmmBuildSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmBuildSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuild_actionPerformed(false);
+ }
+ });
+ JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmbuild"));
+ hmmBuildRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuild_actionPerformed(true);
+ }
+ });
+ hmmBuild.add(hmmBuildRun);
+ hmmBuild.add(hmmBuildSettings);
+
+ /*
+ * hmmalign
+ */
+ JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
+ JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmalign"));
+ hmmAlignRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmAlign_actionPerformed(true);
+ }
+ });
+ JMenuItem hmmAlignSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmAlignSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmAlign_actionPerformed(false);
+ }
+ });
+ hmmAlign.add(hmmAlignRun);
+ hmmAlign.add(hmmAlignSettings);
+
+ /*
+ * hmmsearch
+ */
+ JMenu hmmSearch = new JMenu(
+ MessageManager.getString("label.hmmsearch"));
+ JMenuItem hmmSearchSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmSearchSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmSearch_actionPerformed(false);
+ }
+ });
+ JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmsearch"));
+ hmmSearchRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmSearch_actionPerformed(true);
+ }
+ });
+ JMenuItem addDatabase = new JMenuItem(
+ MessageManager.getString("label.add_database"));
+ addDatabase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ addDatabase_actionPerformed();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ hmmSearch.add(hmmSearchRun);
+ hmmSearch.add(hmmSearchSettings);
+ // hmmSearch.add(addDatabase);
+
+ /*
+ * jackhmmer
+ */
+ JMenu jackhmmer = new JMenu(
+ MessageManager.getString("label.jackhmmer"));
+ JMenuItem jackhmmerSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ jackhmmerSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ jackhmmer_actionPerformed(false);
+ }
+ });
+ JMenuItem jackhmmerRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "jackhmmer"));
+ jackhmmerRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ jackhmmer_actionPerformed(true);
+ }
+
+ });
+ /*
+ JMenuItem addDatabase = new JMenuItem(
+ MessageManager.getString("label.add_database"));
+ addDatabase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ addDatabase_actionPerformed();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ */
+ jackhmmer.add(jackhmmerRun);
+ jackhmmer.add(jackhmmerSettings);
+ // hmmSearch.add(addDatabase);
+
+ /*
+ * top level menu
+ */
+ hmmerMenu.setText(MessageManager.getString("action.hmmer"));
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+ hmmerMenu.add(hmmBuild);
+ hmmerMenu.add(hmmAlign);
+ hmmerMenu.add(hmmSearch);
+ hmmerMenu.add(jackhmmer);
+
+ }
+
+ protected void enableSortMenuOptions()
+ {
+ }
+
protected void loadVcf_actionPerformed()
{
}
{
}
+ protected void sortEValueMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
}
}
protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
{
}
+ protected void hmmBuild_actionPerformed(boolean withDefaults)
+ {
+ }
+
+ protected void hmmSearch_actionPerformed(boolean withDefaults)
+ {
+ }
+
+ protected void jackhmmer_actionPerformed(boolean b)
+ {
+ }
+
+ protected void addDatabase_actionPerformed()
+ throws FileFormatException, IOException
+ {
+ }
+
+ protected void hmmAlign_actionPerformed(boolean withDefaults)
+ {
+ }
+
public void createPNG(java.io.File f)
{
}
{
}
+ protected void filterByEValue_actionPerformed()
+ {
+ }
+
+ protected void filterByScore_actionPerformed()
+ {
+ }
+
protected void scaleRight_actionPerformed(ActionEvent e)
{
}
}
public void associatedData_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
protected void showComplement_actionPerformed(boolean complement)
{
}
+
+
}
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.awt.event.MouseAdapter;
import java.util.Arrays;
import java.util.List;
+import javax.swing.AbstractButton;
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
+import javax.swing.JComponent;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
+import net.miginfocom.swing.MigLayout;
+
/**
* Base class for the Preferences panel.
*
protected JCheckBox showConsensLogo = new JCheckBox();
+ protected JCheckBox showInformationHistogram = new JCheckBox();
+
+ protected JCheckBox showHMMLogo = new JCheckBox();
+
protected JCheckBox showDbRefTooltip = new JCheckBox();
protected JCheckBox showNpTooltip = new JCheckBox();
+
/*
* Structure tab and components
*/
protected JCheckBox sortByTree = new JCheckBox();
/*
+ * hmmer tab and components
+ */
+ protected JPanel hmmerTab;
+
+ protected JCheckBox hmmrTrimTermini;
+
+ protected AbstractButton hmmerBackgroundUniprot;
+
+ protected AbstractButton hmmerBackgroundAlignment;
+
+ protected JTextField hmmerSequenceCount;
+
+ protected JTextField hmmerPath;
+
+ protected JTextField cygwinPath;
+
+ /*
* Web Services tab
*/
protected JPanel wsTab = new JPanel();
+ protected JPanel slivkaTab = new JPanel();
+
/*
* Backups tab components
* a lot of these are member variables instead of local variables only so that they
tabbedPane.add(initEditingTab(),
MessageManager.getString("label.editing"));
+ tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
+
/*
* See WsPreferences for the real work of configuring this tab.
*/
{
wsTab.setLayout(new BorderLayout());
tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+ slivkaTab.setLayout(new BorderLayout());
+ tabbedPane.add(slivkaTab, "Slivka Services");
}
/*
* Handler to validate a tab before leaving it - currently only for
- * Structure.
+ * Structure
*/
tabbedPane.addChangeListener(new ChangeListener()
{
}
/**
- * Initialises the Output tab
+ * Initialises the hmmer tabbed panel
+ *
+ * @return
+ */
+ private JPanel initHMMERTab()
+ {
+ hmmerTab = new JPanel();
+ hmmerTab.setLayout(new BoxLayout(hmmerTab, BoxLayout.Y_AXIS));
+ hmmerTab.setLayout(new MigLayout("flowy"));
+
+ /*
+ * path to hmmer binaries folder
+ */
+ JPanel installationPanel = new JPanel(new MigLayout("flowy"));
+ // new FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(installationPanel,
+ MessageManager.getString("label.installation"), true);
+ hmmerTab.add(installationPanel);
+ JLabel hmmerLocation = new JLabel(
+ MessageManager.getString("label.hmmer_location"));
+ hmmerLocation.setFont(LABEL_FONT);
+ final int pathFieldLength = 40;
+ hmmerPath = new JTextField(pathFieldLength);
+ hmmerPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ hmmerPath.setText(chosen);
+ validateHmmerPath();
+ }
+ }
+ }
+ });
+ installationPanel.add(hmmerLocation);
+ installationPanel.add(hmmerPath);
+
+ /*
+ * path to Cygwin binaries folder (for Windows)
+ */
+ if (Platform.isWindowsAndNotJS())
+ {
+ JLabel cygwinLocation = new JLabel(
+ MessageManager.getString("label.cygwin_location"));
+ cygwinLocation.setFont(LABEL_FONT);
+ cygwinPath = new JTextField(pathFieldLength);
+ cygwinPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ cygwinPath.setText(chosen);
+ validateCygwinPath();
+ }
+ }
+ }
+ });
+ installationPanel.add(cygwinLocation);
+ installationPanel.add(cygwinPath);
+ }
+
+ /*
+ * preferences for hmmalign
+ */
+ JPanel alignOptionsPanel = new JPanel(new MigLayout());
+ // new FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(alignOptionsPanel,
+ MessageManager.getString("label.hmmalign_options"), true);
+ hmmerTab.add(alignOptionsPanel);
+ hmmrTrimTermini = new JCheckBox();
+ hmmrTrimTermini.setFont(LABEL_FONT);
+ hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
+ alignOptionsPanel.add(hmmrTrimTermini);
+
+ /*
+ * preferences for hmmsearch
+ */
+ JPanel searchOptions = new JPanel(new MigLayout());
+ // FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(searchOptions,
+ MessageManager.getString("label.hmmsearch_options"), true);
+ hmmerTab.add(searchOptions);
+ JLabel sequencesToKeep = new JLabel(
+ MessageManager.getString("label.no_of_sequences"));
+ sequencesToKeep.setFont(LABEL_FONT);
+ searchOptions.add(sequencesToKeep);
+ hmmerSequenceCount = new JTextField(5);
+ searchOptions.add(hmmerSequenceCount);
+
+ /*
+ * preferences for Information Content annotation
+ */
+ // JPanel dummy = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ JPanel annotationOptions = new JPanel(new MigLayout("left"));
+ JvSwingUtils.createTitledBorder(annotationOptions,
+ MessageManager.getString("label.information_annotation"), true);
+ // dummy.add(annotationOptions);
+ hmmerTab.add(annotationOptions);
+ ButtonGroup backgroundOptions = new ButtonGroup();
+ hmmerBackgroundUniprot = new JRadioButton(
+ MessageManager.getString("label.freq_uniprot"));
+ hmmerBackgroundUniprot.setFont(LABEL_FONT);
+ hmmerBackgroundAlignment = new JRadioButton(
+ MessageManager.getString("label.freq_alignment"));
+ hmmerBackgroundAlignment.setFont(LABEL_FONT);
+ backgroundOptions.add(hmmerBackgroundUniprot);
+ backgroundOptions.add(hmmerBackgroundAlignment);
+ backgroundOptions.setSelected(hmmerBackgroundUniprot.getModel(), true);
+ // disable buttons for now as annotation only uses Uniprot background
+ hmmerBackgroundAlignment.setEnabled(false);
+ hmmerBackgroundUniprot.setEnabled(false);
+ annotationOptions.add(hmmerBackgroundUniprot, "wrap");
+ annotationOptions.add(hmmerBackgroundAlignment);
+
+ return hmmerTab;
+ }
+
+ /**
+ * Initialises the Output tabbed panel.
*
* @return
*/
protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
protColourLabel.setText(
MessageManager.getString("label.prot_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab,
+ GPreferences.addtoLayout(coloursTab,
MessageManager
.getString("label.default_colour_scheme_for_alignment"),
protColourLabel, protColour);
nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
nucColourLabel.setText(
MessageManager.getString("label.nuc_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab,
+ GPreferences.addtoLayout(coloursTab,
MessageManager
.getString("label.default_colour_scheme_for_alignment"),
nucColourLabel, nucColour);
annotationShding.setBorder(new TitledBorder(
MessageManager.getString("label.annotation_shading_default")));
annotationShding.setLayout(new GridLayout(1, 2));
- JvSwingUtils.addtoLayout(annotationShding,
+ GPreferences.addtoLayout(annotationShding,
MessageManager.getString(
"label.default_minimum_colour_annotation_shading"),
mincolourLabel, minColour);
- JvSwingUtils.addtoLayout(annotationShding,
+ GPreferences.addtoLayout(annotationShding,
MessageManager.getString(
"label.default_maximum_colour_annotation_shading"),
maxcolourLabel, maxColour);
viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
structureTab.add(viewerLabel);
- structViewer.setFont(LABEL_FONT);
- structViewer.setBounds(new Rectangle(160, ypos, 120, height));
- structViewer.addItem(ViewerType.JMOL.name());
- structViewer.addItem(ViewerType.CHIMERA.name());
- structViewer.addActionListener(new ActionListener()
+ if (!Platform.isJS())
{
- @Override
- public void actionPerformed(ActionEvent e)
+ structViewer.setFont(LABEL_FONT);
+ structViewer.setBounds(new Rectangle(160, ypos, 120, height));
+ structViewer.addItem(ViewerType.JMOL.name());
+ structViewer.addItem(ViewerType.CHIMERA.name());
+ structViewer.addActionListener(new ActionListener()
{
- structureViewer_actionPerformed(
- (String) structViewer.getSelectedItem());
- }
- });
- structureTab.add(structViewer);
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ structureViewer_actionPerformed(
+ (String) structViewer.getSelectedItem());
+ }
+ });
+ structureTab.add(structViewer);
+ }
ypos += lineSpacing;
JLabel pathLabel = new JLabel();
{
if (e.getClickCount() == 2)
{
- String chosen = openFileChooser();
+ String chosen = openFileChooser(false);
if (chosen != null)
{
chimeraPath.setText(chosen);
/*
* hide Chimera options in JalviewJS
*/
- if (Platform.isJS())
+ if (Platform.isJS())
{
pathLabel.setVisible(false);
chimeraPath.setVisible(false);
viewerLabel.setVisible(false);
structViewer.setVisible(false);
}
-
+
return structureTab;
}
*
* @return
*/
- protected String openFileChooser()
+ protected String openFileChooser(boolean forFolder)
{
String choice = null;
JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
// chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
return choice;
}
- /**
- * Validate the structure tab preferences; if invalid, set focus on this tab.
- *
- * @param e
- */
- protected boolean validateStructure(FocusEvent e)
- {
- if (!validateStructure())
- {
- e.getComponent().requestFocusInWindow();
- return false;
- }
- return true;
- }
-
protected boolean validateStructure()
{
return false;
boolean ret = false;
String warningMessage = MessageManager
.getString("label.warning_confirm_change_reverse");
- int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ int confirm = JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(),
warningMessage,
MessageManager.getString("label.change_increment_decrement"),
JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
}
}
+
+ protected void validateHmmerPath()
+ {
+ }
+
+ protected void validateCygwinPath()
+ {
+ }
+
+ /**
+ * A helper method to add a panel containing a label and a component to a
+ * panel
+ *
+ * @param panel
+ * @param tooltip
+ * @param label
+ * @param valBox
+ */
+ protected static void addtoLayout(JPanel panel, String tooltip,
+ JComponent label, JComponent valBox)
+ {
+ JPanel laypanel = new JPanel(new GridLayout(1, 2));
+ JPanel labPanel = new JPanel(new BorderLayout());
+ JPanel valPanel = new JPanel();
+ labPanel.setBounds(new Rectangle(7, 7, 158, 23));
+ valPanel.setBounds(new Rectangle(172, 7, 270, 23));
+ labPanel.add(label, BorderLayout.WEST);
+ valPanel.add(valBox);
+ laypanel.add(labPanel);
+ laypanel.add(valPanel);
+ valPanel.setToolTipText(tooltip);
+ labPanel.setToolTipText(tooltip);
+ valBox.setToolTipText(tooltip);
+ panel.add(laypanel);
+ panel.validate();
+ }
}
import jalview.analysis.PCA;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.SimilarityParams;
+ import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
import jalview.gui.AppVarna;
import jalview.gui.ChimeraViewFrame;
import jalview.gui.Desktop;
+ import jalview.gui.FeatureRenderer;
import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
import jalview.gui.PCAPanel;
import jalview.io.BackupFiles;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
+import jalview.io.HMMFile;
import jalview.io.NewickFile;
import jalview.math.Matrix;
import jalview.math.MatrixI;
import jalview.schemes.FeatureColour;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
- import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.Format;
import jalview.util.MessageManager;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
-import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.jws2.PreferredServiceRegistry;
import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
import jalview.xml.binding.jalview.VAMSAS;
import java.awt.Color;
+ import java.awt.Dimension;
import java.awt.Font;
import java.awt.Rectangle;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
+ import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
- import java.lang.reflect.InvocationTargetException;
import java.math.BigInteger;
import java.net.MalformedURLException;
import java.net.URL;
private static final String RNA_PREFIX = "rna_";
+ private static final String HMMER_PREFIX = "hmmer_";
+
private static final String UTF_8 = "UTF-8";
/**
private Map<RnaModel, String> rnaSessions = new HashMap<>();
/**
+ * contains last error message (if any) encountered by XML loader.
+ */
+ String errorMessage = null;
+
+ /**
+ * flag to control whether the Jalview2XML_V1 parser should be deferred to if
+ * exceptions are raised during project XML parsing
+ */
+ public boolean attemptversion1parse = false;
+
+ /*
+ * JalviewJS only -- to allow read file bytes to be saved in the
+ * created AlignFrame, allowing File | Reload of a project file to work
+ *
+ * BH 2019 JAL-3436
+ */
+ private File jarFile;
+
+ /**
* A helper method for safely using the value of an optional attribute that
* may be null if not present in the XML. Answers the boolean value, or false
* if null.
* @param _jmap
* @return
*/
- public SeqFref newMappingRef(final String sref,
+ protected SeqFref newMappingRef(final String sref,
final jalview.datamodel.Mapping _jmap)
{
SeqFref fref = new SeqFref(sref, "Mapping")
return fref;
}
- public SeqFref newAlcodMapRef(final String sref,
+ protected SeqFref newAlcodMapRef(final String sref,
final AlignedCodonFrame _cf,
final jalview.datamodel.Mapping _jmap)
{
return fref;
}
- public void resolveFrefedSequences()
+ protected void resolveFrefedSequences()
{
Iterator<SeqFref> nextFref = frefedSequence.iterator();
int toresolve = frefedSequence.size();
* core method for storing state for a set of AlignFrames.
*
* @param frames
- * - frames involving all data to be exported (including containing
- * splitframes)
+ * - frames involving all data to be exported (including those
+ * contained in splitframes, though not the split frames themselves)
* @param jout
* - project output stream
*/
private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
{
+
Hashtable<String, AlignFrame> dsses = new Hashtable<>();
/*
for (int i = frames.size() - 1; i > -1; i--)
{
AlignFrame af = frames.get(i);
+ AlignViewport vp = af.getViewport();
// skip ?
if (skipList != null && skipList
- .containsKey(af.getViewport().getSequenceSetId()))
+ .containsKey(vp.getSequenceSetId()))
{
continue;
}
String shortName = makeFilename(af, shortNames);
- int apSize = af.getAlignPanels().size();
-
+ AlignmentI alignment = vp.getAlignment();
+ List<? extends AlignmentViewPanel> panels = af.getAlignPanels();
+ int apSize = panels.size();
for (int ap = 0; ap < apSize; ap++)
- {
- AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
- .get(ap);
+ {
+ AlignmentPanel apanel = (AlignmentPanel) panels.get(ap);
String fileName = apSize == 1 ? shortName : ap + shortName;
if (!fileName.endsWith(".xml"))
{
}
saveState(apanel, fileName, jout, viewIds);
-
- String dssid = getDatasetIdRef(
- af.getViewport().getAlignment().getDataset());
+ }
+ if (apSize > 0)
+ {
+ // BH moved next bit out of inner loop, not that it really matters.
+ // so we are testing to make sure we actually have an alignment,
+ // apparently.
+ String dssid = getDatasetIdRef(alignment.getDataset());
if (!dsses.containsKey(dssid))
{
+ // We have not already covered this data by reference from another
+ // frame.
dsses.put(dssid, af);
}
}
}
}
+ /**
+ * Each AlignFrame has a single data set associated with it. Note that none of
+ * these frames are split frames, because Desktop.getAlignFrames() collects
+ * top and bottom separately here.
+ *
+ * @param dsses
+ * @param fileName
+ * @param jout
+ */
private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
String fileName, JarOutputStream jout)
{
+ // Note that in saveAllFrames we have associated each specific dataset to
+ // ONE of its associated frames.
+
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
* @param out
* jar entry name
*/
- public JalviewModel saveState(AlignmentPanel ap, String fileName,
+ protected JalviewModel saveState(AlignmentPanel ap, String fileName,
JarOutputStream jout, List<String> viewIds)
{
return saveState(ap, fileName, false, jout, viewIds);
* @param out
* jar entry name
*/
- public JalviewModel saveState(AlignmentPanel ap, String fileName,
+ protected JalviewModel saveState(AlignmentPanel ap, String fileName,
boolean storeDS, JarOutputStream jout, List<String> viewIds)
{
if (viewIds == null)
jseq.getFeatures().add(features);
}
+ /*
+ * save PDB entries for sequence
+ */
if (jdatasq.getAllPDBEntries() != null)
{
Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
* only view *should* be coped with sensibly.
*/
// This must have been loaded, is it still visible?
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
String matchedFile = null;
for (int f = frames.length - 1; f > -1; f--)
{
saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
+ if (jds.hasHMMProfile())
+ {
+ saveHmmerProfile(jout, jseq, jds);
+ }
+
// jms.addJSeq(jseq);
object.getJSeq().add(jseq);
}
{
// FIND ANY ASSOCIATED TREES
// NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
for (int t = 0; t < frames.length; t++)
{
/*
* save PCA viewers
*/
- if (!storeDS && Desktop.desktop != null)
+ if (!storeDS && Desktop.getDesktopPane() != null)
{
- for (JInternalFrame frame : Desktop.desktop.getAllFrames())
+ for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
{
if (frame instanceof PCAPanel)
{
}
return object;
}
+ /**
+ * Saves the HMMER profile associated with the sequence as a file in the jar,
+ * in HMMER format, and saves the name of the file as a child element of the
+ * XML sequence element
+ *
+ * @param jout
+ * @param xmlSeq
+ * @param seq
+ */
+ protected void saveHmmerProfile(JarOutputStream jout, JSeq xmlSeq,
+ SequenceI seq)
+ {
+ HiddenMarkovModel profile = seq.getHMM();
+ if (profile == null)
+ {
+ warn("Want to save HMM profile for " + seq.getName()
+ + " but none found");
+ return;
+ }
+ HMMFile hmmFile = new HMMFile(profile);
+ String hmmAsString = hmmFile.print();
+ String jarEntryName = HMMER_PREFIX + nextCounter();
+ try
+ {
+ writeJarEntry(jout, jarEntryName, hmmAsString.getBytes());
+ xmlSeq.setHmmerProfile(jarEntryName);
+ } catch (IOException e)
+ {
+ warn("Error saving HMM profile: " + e.getMessage());
+ }
+ }
+
/**
* Writes PCA viewer attributes and computed values to an XML model object and
* adds it to the JalviewModel. Any exceptions are reported by logging.
final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
boolean storeDataset)
{
- if (Desktop.desktop == null)
+ if (Desktop.getDesktopPane() == null)
{
return;
}
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
for (int f = frames.length - 1; f > -1; f--)
{
if (frames[f] instanceof AppVarna)
}
else if (!matchedFile.equals(pdbentry.getFile()))
{
- Cache.log.warn(
- "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
- + pdbentry.getFile());
+ Cache.log.warn(
+ "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ + pdbentry.getFile());
}
// record the
// file so we
if (calcIdParam.getVersion().equals("1.0"))
{
final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
- Jws2Instance service = Jws2Discoverer.getInstance()
+ ServiceWithParameters service = PreferredServiceRegistry.getRegistry()
.getPreferredServiceFor(calcIds);
if (service != null)
{
argList = parmSet.getArguments();
parmSet = null;
}
- AAConSettings settings = new AAConSettings(
+ AutoCalcSetting settings = new AAConSettings(
calcIdParam.isAutoUpdate(), service, parmSet, argList);
av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
calcIdParam.isNeedsUpdate());
}
else
{
- warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ warn("Cannot resolve a service for the parameters used in this project. Try configuring a server in the Web Services preferences tab.");
return false;
}
}
}
/**
- * contains last error message (if any) encountered by XML loader.
- */
- String errorMessage = null;
-
- /**
- * flag to control whether the Jalview2XML_V1 parser should be deferred to if
- * exceptions are raised during project XML parsing
- */
- public boolean attemptversion1parse = false;
-
- /**
* Load a jalview project archive from a jar file
*
* @param file
{
try
{
- SwingUtilities.invokeAndWait(new Runnable()
+ // was invokeAndWait
+
+ // BH 2019 -- can't wait
+ SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
System.err.println("Error loading alignment: " + x.getMessage());
}
}
+ this.jarFile = null;
return af;
}
@SuppressWarnings("unused")
- private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
-
- // BH 2018 allow for bytes already attached to File object
- try {
- String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
+ private jarInputStreamProvider createjarInputStreamProvider(
+ final Object ofile) throws MalformedURLException
+ {
+ try
+ {
+ String file = (ofile instanceof File
+ ? ((File) ofile).getCanonicalPath()
+ : ofile.toString());
byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
: null;
- URL url = null;
- errorMessage = null;
- uniqueSetSuffix = null;
- seqRefIds = null;
- viewportsAdded.clear();
- frefedSequence = null;
-
- if (file.startsWith("http://")) {
- url = new URL(file);
- }
- final URL _url = url;
- return new jarInputStreamProvider() {
-
- @Override
- public JarInputStream getJarInputStream() throws IOException {
- if (bytes != null) {
- // System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
- return new JarInputStream(new ByteArrayInputStream(bytes));
- }
- if (_url != null) {
- // System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
- return new JarInputStream(_url.openStream());
- } else {
- // System.out.println("Jalview2XML: opening file jarInputStream for " + file);
- return new JarInputStream(new FileInputStream(file));
- }
- }
-
- @Override
- public String getFilename() {
- return file;
- }
- };
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
+ if (bytes != null)
+ {
+ this.jarFile = (File) ofile;
+ }
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded.clear();
+ frefedSequence = null;
+
+ URL url = file.startsWith("http://") ? new URL(file) : null;
+ return new jarInputStreamProvider()
+ {
+ @Override
+ public JarInputStream getJarInputStream() throws IOException
+ {
+ InputStream is = bytes != null ? new ByteArrayInputStream(bytes)
+ : (url != null ? url.openStream()
+ : new FileInputStream(file));
+ return new JarInputStream(is);
+ }
+
+ @Override
+ public File getFile()
+ {
+ return jarFile;
+ }
+
+ @Override
+ public String getFilename()
+ {
+ return file;
+ }
+ };
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ return null;
+ }
+ }
/**
* Recover jalview session from a jalview project archive. Caller may
AlignFrame af = null, _af = null;
IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
- final String file = jprovider.getFilename();
+ String fileName = jprovider.getFilename();
+ File file = jprovider.getFile();
+ List<AlignFrame> alignFrames = new ArrayList<>();
+
try
{
JarInputStream jin = null;
JarEntry jarentry = null;
int entryCount = 1;
+
+ // Look for all the entry names ending with ".xml"
+ // This includes all panels and at least one frame.
+ // Platform.timeCheck(null, Platform.TIME_MARK);
do
{
jin = jprovider.getJarInputStream();
{
jarentry = jin.getNextJarEntry();
}
+ String name = (jarentry == null ? null : jarentry.getName());
- if (jarentry != null && jarentry.getName().endsWith(".xml"))
+ // System.out.println("Jalview2XML opening " + name);
+ if (name != null && name.endsWith(".xml"))
{
+
+ // DataSet for.... is read last.
+
+
+ // The question here is what to do with the two
+ // .xml files in the jvp file.
+ // Some number of them, "...Dataset for...", will be the
+ // Only AlignPanels and will have Viewport.
+ // One or more will be the source data, with the DBRefs.
+ //
+ // JVP file writing (above) ensures tha the AlignPanels are written
+ // first, then all relevant datasets (which are
+ // Jalview.datamodel.Alignment).
+ //
+
+ // Platform.timeCheck("Jalview2XML JAXB " + name, Platform.TIME_MARK);
JAXBContext jc = JAXBContext
.newInstance("jalview.xml.binding.jalview");
XMLStreamReader streamReader = XMLInputFactory.newInstance()
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
JAXBElement<JalviewModel> jbe = um
.unmarshal(streamReader, JalviewModel.class);
- JalviewModel object = jbe.getValue();
+ JalviewModel model = jbe.getValue();
if (true) // !skipViewport(object))
{
- _af = loadFromObject(object, file, true, jprovider);
- if (_af != null && object.getViewport().size() > 0)
- // getJalviewModelSequence().getViewportCount() > 0)
+ // Q: Do we have to load from the model, even if it
+ // does not have a viewport, could we discover that early on?
+ // Q: Do we need to load this object?
+ _af = loadFromObject(model, fileName, file, true, jprovider);
+ // Platform.timeCheck("Jalview2XML.loadFromObject",
+ // Platform.TIME_MARK);
+
+ if (_af != null)
+ {
+ alignFrames.add(_af);
+ }
+ if (_af != null && model.getViewport().size() > 0)
{
+
+ // That is, this is one of the AlignmentPanel models
if (af == null)
{
// store a reference to the first view
} catch (IOException ex)
{
ex.printStackTrace();
- errorMessage = "Couldn't locate Jalview XML file : " + file;
+ errorMessage = "Couldn't locate Jalview XML file : " + fileName;
System.err.println(
"Exception whilst loading jalview XML file : " + ex + "\n");
} catch (Exception ex)
{
// used to attempt to parse as V1 castor-generated xml
}
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
if (af != null)
{
errorMessage = "Out of memory loading jalview XML file";
System.err.println("Out of memory whilst loading jalview XML file");
e.printStackTrace();
+ } finally
+ {
+ for (AlignFrame alf : alignFrames)
+ {
+ alf.alignPanel.setHoldRepaint(false);
+ }
+
}
/*
*/
for (AlignFrame fr : gatherToThisFrame.values())
{
- Desktop.instance.gatherViews(fr);
+ Desktop.getInstance().gatherViews(fr);
}
restoreSplitFrames();
{
if (ds.getCodonFrames() != null)
{
- StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ Desktop.getStructureSelectionManager()
.registerMappings(ds.getCodonFrames());
}
}
reportErrors();
}
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
return af;
*/
for (SplitFrame sf : gatherTo)
{
- Desktop.instance.gatherViews(sf);
+ Desktop.getInstance().gatherViews(sf);
}
splitFrameCandidates.clear();
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
finalErrorMessage,
"Error " + (saving ? "saving" : "loading")
+ " Jalview file",
* @param prefix
* a prefix for the temporary file name, must be at least three
* characters long
- * @param suffixModel
+ * @param origFile
* null or original file - so new file can be given the same suffix
* as the old one
* @return
*/
protected String copyJarEntry(jarInputStreamProvider jprovider,
- String jarEntryName, String prefix, String suffixModel)
+ String jarEntryName, String prefix, String origFile)
{
BufferedReader in = null;
PrintWriter out = null;
String suffix = ".tmp";
- if (suffixModel == null)
+ if (origFile == null)
{
- suffixModel = jarEntryName;
+ origFile = jarEntryName;
}
- int sfpos = suffixModel.lastIndexOf(".");
- if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
+ int sfpos = origFile.lastIndexOf(".");
+ if (sfpos > -1 && sfpos < (origFile.length() - 3))
{
- suffix = "." + suffixModel.substring(sfpos + 1);
+ suffix = "." + origFile.substring(sfpos + 1);
}
try
{
}
/**
- * Load alignment frame from jalview XML DOM object
+ * Load alignment frame from jalview XML DOM object. For a DOM object that
+ * includes one or more Viewport elements (one with a title that does NOT
+ * contain "Dataset for"), create the frame.
*
* @param jalviewModel
* DOM
- * @param file
+ * @param fileName
* filename source string
+ * @param file
* @param loadTreesAndStructures
* when false only create Viewport
* @param jprovider
* data source provider
* @return alignment frame created from view stored in DOM
*/
- AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
- boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
+ AlignFrame loadFromObject(JalviewModel jalviewModel, String fileName,
+ File file, boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
List<Sequence> vamsasSeqs = vamsasSet.getSequence();
+
// JalviewModelSequence jms = object.getJalviewModelSequence();
// Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
{
entry.setProperty(prop.getName(), prop.getValue());
}
- StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ Desktop.getStructureSelectionManager()
.registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
if (al.getSequenceAt(i).getDatasetSequence() != null)
}
}
+ /*
+ * load any HMMER profile
+ */
+ // TODO fix this
+
+ String hmmJarFile = jseqs.get(i).getHmmerProfile();
+ if (hmmJarFile != null && jprovider != null)
+ {
+ loadHmmerProfile(jprovider, hmmJarFile, al.getSequenceAt(i));
+ }
-
}
} // end !multipleview
}
}
}
+ // create the new AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation jaa = null;
if (annotation.isGraph())
jaa._linecolour = firstColour;
}
// register new annotation
+ // Annotation graphs such as Conservation will not have id.
if (annotation.getId() != null)
{
annotationIds.put(annotation.getId(), jaa);
// ///////////////////////////////
// LOAD VIEWPORT
- AlignFrame af = null;
- AlignViewport av = null;
// now check to see if we really need to create a new viewport.
if (multipleView && viewportsAdded.size() == 0)
{
boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
jalviewModel.getVersion());
+ AlignFrame af = null;
AlignmentPanel ap = null;
- boolean isnewview = true;
+ AlignViewport av = null;
if (viewId != null)
{
// Check to see if this alignment already has a view id == viewId
{
for (int v = 0; v < views.length; v++)
{
- if (views[v].av.getViewId().equalsIgnoreCase(viewId))
+ ap = views[v];
+ av = ap.av;
+ if (av.getViewId().equalsIgnoreCase(viewId))
{
// recover the existing alignpanel, alignframe, viewport
- af = views[v].alignFrame;
- av = views[v].av;
- ap = views[v];
+ af = ap.alignFrame;
+ break;
// TODO: could even skip resetting view settings if we don't want to
// change the local settings from other jalview processes
- isnewview = false;
}
}
}
}
- if (isnewview)
+ if (af == null)
{
- af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
+ af = loadViewport(fileName, file, jseqs, hiddenSeqs, al, jalviewModel, view,
uniqueSeqSetId, viewId, autoAlan);
av = af.getViewport();
+ // note that this only retrieves the most recently accessed
+ // tab of an AlignFrame.
ap = af.alignPanel;
}
*
* Not done if flag is false (when this method is used for New View)
*/
+ final AlignFrame af0 = af;
+ final AlignViewport av0 = av;
+ final AlignmentPanel ap0 = ap;
+ // Platform.timeCheck("Jalview2XML.loadFromObject-beforetree",
+ // Platform.TIME_MARK);
if (loadTreesAndStructures)
{
- loadTrees(jalviewModel, view, af, av, ap);
- loadPCAViewers(jalviewModel, ap);
- loadPDBStructures(jprovider, jseqs, af, ap);
- loadRnaViewers(jprovider, jseqs, ap);
+ if (!jalviewModel.getTree().isEmpty())
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ // Platform.timeCheck(null, Platform.TIME_MARK);
+ loadTrees(jalviewModel, view, af0, av0, ap0);
+ // Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK);
+ }
+ });
+ }
+ if (!jalviewModel.getPcaViewer().isEmpty())
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ // Platform.timeCheck(null, Platform.TIME_MARK);
+ loadPCAViewers(jalviewModel, ap0);
+ // Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK);
+ }
+ });
+ }
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ // Platform.timeCheck(null, Platform.TIME_MARK);
+ loadPDBStructures(jprovider, jseqs, af0, ap0);
+ // Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK);
+ }
+ });
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ loadRnaViewers(jprovider, jseqs, ap0);
+ }
+ });
}
// and finally return.
+ // but do not set holdRepaint true just yet, because this could be the
+ // initial frame with just its dataset.
return af;
}
/**
+ * Loads a HMMER profile from a file stored in the project, and associates it
+ * with the specified sequence
+ *
+ * @param jprovider
+ * @param hmmJarFile
+ * @param seq
+ */
+ protected void loadHmmerProfile(jarInputStreamProvider jprovider,
+ String hmmJarFile, SequenceI seq)
+ {
+ try
+ {
+ String hmmFile = copyJarEntry(jprovider, hmmJarFile, "hmm", null);
+ HMMFile parser = new HMMFile(hmmFile, DataSourceType.FILE);
+ HiddenMarkovModel hmmModel = parser.getHMM();
+ hmmModel = new HiddenMarkovModel(hmmModel, seq);
+ seq.setHMM(hmmModel);
+ } catch (IOException e)
+ {
+ warn("Error loading HMM profile for " + seq.getName() + ": "
+ + e.getMessage());
+ }
+ }
+
+ /**
* Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
* panel is restored from separate jar entries, two (gapped and trimmed) per
* sequence and secondary structure.
* @param jseqs
* @param ap
*/
- private void loadRnaViewers(jarInputStreamProvider jprovider,
+ protected void loadRnaViewers(jarInputStreamProvider jprovider,
List<JSeq> jseqs, AlignmentPanel ap)
{
/*
tree.getTitle(), safeInt(tree.getWidth()),
safeInt(tree.getHeight()), safeInt(tree.getXpos()),
safeInt(tree.getYpos()));
+ if (tp == null)
+ {
+ warn("There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
+ continue;
+ }
if (tree.getId() != null)
{
// perhaps bind the tree id to something ?
tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
}
tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
- if (tp == null)
- {
- warn("There was a problem recovering stored Newick tree: \n"
- + tree.getNewick());
- continue;
- }
-
tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
tp.fitToWindow_actionPerformed(null);
int height = safeInt(structureState.getHeight());
// Probably don't need to do this anymore...
- // Desktop.desktop.getComponentAt(x, y);
+ // Desktop.getDesktop().getComponentAt(x, y);
// TODO: NOW: check that this recovers the PDB file correctly.
String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
pdbid.getFile());
String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
filedat = oldFiles.get(new File(reformatedOldFilename));
}
- newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
+ newFileLoc
+ .append(Platform.escapeBackslashes(filedat.getFilePath()));
pdbfilenames.add(filedat.getFilePath());
pdbids.add(filedat.getPdbId());
seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
final AlignFrame alf = af;
final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
svattrib.getWidth(), svattrib.getHeight());
- try
- {
- javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+
+ // BH again was invokeAndWait
+ // try
+ // {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
}
}
});
- } catch (InvocationTargetException ex)
- {
- warn("Unexpected error when opening Jmol view.", ex);
-
- } catch (InterruptedException e)
- {
- // e.printStackTrace();
- }
+ // } catch (InvocationTargetException ex)
+ // {
+ // warn("Unexpected error when opening Jmol view.", ex);
+ //
+ // } catch (InterruptedException e)
+ // {
+ // // e.printStackTrace();
+ // }
}
{
try
{
- frames = Desktop.desktop.getAllFrames();
+ frames = Desktop.getDesktopPane().getAllFrames();
} catch (ArrayIndexOutOfBoundsException e)
{
// occasional No such child exceptions are thrown here...
}
}
- AlignFrame loadViewport(String file, List<JSeq> JSEQ,
- List<SequenceI> hiddenSeqs, AlignmentI al,
- JalviewModel jm, Viewport view, String uniqueSeqSetId,
- String viewId, List<JvAnnotRow> autoAlan)
+ AlignFrame loadViewport(String fileName, File file, List<JSeq> JSEQ,
+ List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
+ Viewport view, String uniqueSeqSetId, String viewId,
+ List<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
af = new AlignFrame(al, safeInt(view.getWidth()),
- safeInt(view.getHeight()), uniqueSeqSetId, viewId)
- // {
- //
- // @Override
- // protected void processKeyEvent(java.awt.event.KeyEvent e) {
- // System.out.println("Jalview2XML AF " + e);
- // super.processKeyEvent(e);
- //
- // }
- //
- // }
+ safeInt(view.getHeight()), uniqueSeqSetId, viewId)
+ // {
+ //
+ // @Override
+ // protected void processKeyEvent(java.awt.event.KeyEvent e) {
+ // System.out.println("Jalview2XML AF " + e);
+ // super.processKeyEvent(e);
+ //
+ // }
+ //
+ // }
;
-
- af.setFileName(file, FileFormat.Jalview);
+ af.alignPanel.setHoldRepaint(true);
+ af.setFile(fileName, file, null, FileFormat.Jalview);
+ af.setFileObject(jarFile); // BH 2019 JAL-3436
final AlignViewport viewport = af.getViewport();
for (int i = 0; i < JSEQ.size(); i++)
viewport.setColourText(safeBoolean(view.isShowColourText()));
- viewport
- .setConservationSelected(
- safeBoolean(view.isConservationSelected()));
+ viewport.setConservationSelected(
+ safeBoolean(view.isConservationSelected()));
viewport.setIncrement(safeInt(view.getConsThreshold()));
viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
viewport.setViewName(view.getViewName());
af.setInitialTabVisible();
}
- af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
- safeInt(view.getWidth()), safeInt(view.getHeight()));
+ int x = safeInt(view.getXpos());
+ int y = safeInt(view.getYpos());
+ int w = safeInt(view.getWidth());
+ int h = safeInt(view.getHeight());
+ // // BH we cannot let the title bar go off the top
+ // if (Platform.isJS())
+ // {
+ // x = Math.max(50 - w, x);
+ // y = Math.max(0, y);
+ // }
+
+ af.setBounds(x, y, w, h);
// startSeq set in af.alignPanel.updateLayout below
af.alignPanel.updateLayout();
ColourSchemeI cs = null;
af.changeColour(cs);
viewport.setColourAppliesToAllGroups(true);
- viewport
- .setShowSequenceFeatures(
- safeBoolean(view.isShowSequenceFeatures()));
+ viewport.setShowSequenceFeatures(
+ safeBoolean(view.isShowSequenceFeatures()));
viewport.setCentreColumnLabels(view.isCentreColumnLabels());
viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
// recover feature settings
if (jm.getFeatureSettings() != null)
{
- FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
+ FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
.getFeatureRenderer();
FeaturesDisplayed fdi;
viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
- String[] renderOrder = new String[jm.getFeatureSettings()
- .getSetting().size()];
+ String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
+ .size()];
Map<String, FeatureColourI> featureColours = new Hashtable<>();
Map<String, Float> featureOrder = new Hashtable<>();
- for (int fs = 0; fs < jm.getFeatureSettings()
- .getSetting().size(); fs++)
+ for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
+ .size(); fs++)
{
Setting setting = jm.getFeatureSettings().getSetting().get(fs);
String featureType = setting.getType();
.getMatcherSet();
if (filters != null)
{
- FeatureMatcherSetI filter = Jalview2XML
- .parseFilter(featureType, filters);
+ FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
+ filters);
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
float max = setting.getMax() == null ? 1f
: setting.getMax().floatValue();
FeatureColourI gc = new FeatureColour(maxColour, minColour,
- maxColour,
- noValueColour, min, max);
+ maxColour, noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
gc.setAttributeName(setting.getAttributeName().toArray(
}
else
{
- featureColours.put(featureType,
- new FeatureColour(maxColour));
+ featureColours.put(featureType, new FeatureColour(maxColour));
}
renderOrder[fs] = featureType;
if (setting.getOrder() != null)
String complementaryViewId = view.getComplementId();
if (complementaryViewId == null)
{
- Desktop.addInternalFrame(af, view.getTitle(),
+ Dimension dim = Platform.getDimIfEmbedded(af,
safeInt(view.getWidth()), safeInt(view.getHeight()));
+ Desktop.addInternalFrame(af, view.getTitle(), dim.width, dim.height);
// recompute any autoannotation
af.alignPanel.updateAnnotation(false, true);
reorderAutoannotation(af, al, autoAlan);
String id = object.getViewport().get(0).getSequenceSetId();
if (skipList.containsKey(id))
{
- if (Cache.log != null && Cache.log.isDebugEnabled())
- {
- Cache.log.debug("Skipping seuqence set id " + id);
- }
+ if (Cache.log != null && Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Skipping seuqence set id " + id);
+ }
return true;
}
return false;
}
- public void addToSkipList(AlignFrame af)
+ protected void addToSkipList(AlignFrame af)
{
if (skipList == null)
{
skipList.put(af.getViewport().getSequenceSetId(), af);
}
- public void clearSkipList()
+ protected void clearSkipList()
{
if (skipList != null)
{
SequenceI[] dsseqs = new SequenceI[dseqs.size()];
dseqs.copyInto(dsseqs);
ds = new jalview.datamodel.Alignment(dsseqs);
- debug("Created new dataset " + vamsasSet.getDatasetId()
- + " for alignment " + System.identityHashCode(al));
+ // debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId()
+ // + " for alignment " + System.identityHashCode(al));
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
// set the dataset for the newly imported alignment.
jmap.setTo(djs);
incompleteSeqs.put(sqid, djs);
seqRefIds.put(sqid, djs);
-
}
jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
addDBRefs(djs, ms);
viewportsAdded.clear();
- AlignFrame af = loadFromObject(jm, null, false, null);
+ AlignFrame af = loadFromObject(jm, null, null, false, null);
af.getAlignPanels().clear();
af.closeMenuItem_actionPerformed(true);
+ af.alignPanel.setHoldRepaint(false);
+ this.jarFile = null;
/*
* if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
}
else
{
- Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
}
}
}
axis.getXPos(), axis.getYPos(), axis.getZPos());
}
+ Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
Desktop.addInternalFrame(panel, MessageManager.formatMessage(
- "label.calc_title", "PCA", modelName), 475, 450);
+ "label.calc_title", "PCA", modelName), dim.width,
+ dim.height);
}
} catch (Exception ex)
{
maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
} catch (Exception e)
{
- Cache.log.warn("Couldn't parse out graduated feature color.", e);
+ Cache.log.warn("Couldn't parse out graduated feature color.", e);
}
NoValueColour noCol = colourModel.getNoValueColour();
*/
package jalview.util;
- import jalview.javascript.json.JSON;
-
+ import java.awt.Component;
+ import java.awt.Dimension;
+ import java.awt.GraphicsEnvironment;
import java.awt.Toolkit;
+ import java.awt.event.KeyEvent;
import java.awt.event.MouseEvent;
import java.io.BufferedReader;
import java.io.File;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
+ import java.lang.reflect.Method;
import java.net.URL;
+ import java.nio.channels.Channels;
+ import java.nio.channels.ReadableByteChannel;
+ import java.nio.file.Files;
+ import java.nio.file.Path;
+ import java.nio.file.Paths;
+ import java.nio.file.StandardCopyOption;
+ import java.nio.file.attribute.BasicFileAttributes;
+ import java.util.Date;
+ import java.util.Locale;
+ import java.util.Map;
import java.util.Properties;
+ import java.util.logging.ConsoleHandler;
+ import java.util.logging.Level;
+ import java.util.logging.Logger;
import javax.swing.SwingUtilities;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
+ import com.stevesoft.pat.Regex;
+
+ import jalview.bin.Jalview;
+ import jalview.javascript.json.JSON;
+ import swingjs.api.JSUtilI;
+
/**
* System platform information used by Applet and Application
*
private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
isWin = null;
- private static Boolean isHeadless = null;
+ private static swingjs.api.JSUtilI jsutil;
+
+ static
+ {
+ if (isJS)
+ {
+ try
+ {
+ // this is ok - it's a highly embedded method in Java; the deprecation
+ // is
+ // really a recommended best practice.
+ jsutil = ((JSUtilI) Class.forName("swingjs.JSUtil").newInstance());
+ } catch (InstantiationException | IllegalAccessException
+ | ClassNotFoundException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
/**
* added to group mouse events into Windows and nonWindows (mac, unix, linux)
: isMac);
}
+ public static int SHORTCUT_KEY_MASK = (Platform.isMac()
+ ? KeyEvent.META_DOWN_MASK
+ : KeyEvent.CTRL_DOWN_MASK);
+
+ static
+ {
+ if (!GraphicsEnvironment.isHeadless())
+ {
+ // Using non-deprecated Extended key mask modifiers, but Java 8 has no
+ // getMenuShortcutKeyMaskEx method
+ Toolkit tk = Toolkit.getDefaultToolkit();
+ Method method = null;
+ try
+ {
+ method = tk.getClass().getMethod("getMenuShortcutKeyMaskEx");
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Could not find Toolkit method getMenuShortcutKeyMaskEx. Trying getMenuShortcutKeyMask.");
+ }
+ if (method == null)
+ {
+ try
+ {
+ method = tk.getClass().getMethod("getMenuShortcutKeyMask");
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Could not find Toolkit method getMenuShortcutKeyMaskEx or getMenuShortcutKeyMask.");
+ e.printStackTrace();
+ }
+ }
+ if (method != null)
+ {
+ try
+ {
+ method.setAccessible(true);
+ SHORTCUT_KEY_MASK = ((int) method.invoke(tk, new Object[0]));
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ if (SHORTCUT_KEY_MASK <= 0xF)
+ {
+ // shift this into the extended region (was Java 8)
+ SHORTCUT_KEY_MASK = SHORTCUT_KEY_MASK << 6;
+ }
+ }
+ }
/**
* added to group mouse events into Windows and nonWindows (mac, unix, linux)
*
}
/**
- * Check if we are on a Microsoft plaform...
+ * Check if we are on a Microsoft platform...
*
* @return true if we have to cope with another platform variation
*/
return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
}
- /**
- *
- * @return true if we are running in non-interactive no UI mode
- */
- public static boolean isHeadless()
- {
- if (isHeadless == null)
- {
- isHeadless = "true".equals(System.getProperty("java.awt.headless"));
- }
- return isHeadless;
- }
/**
*
*/
protected static boolean isControlDown(MouseEvent e, boolean aMac)
{
- if (!aMac)
- {
- return e.isControlDown();
-
- // Jalview 2.11 code below: above is as amended for JalviewJS
- // /*
- // * answer false for right mouse button
- // */
- // if (e.isPopupTrigger())
- // {
- // return false;
- // }
- // return
- // (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() //
- // .getMenuShortcutKeyMaskEx()
- // & jalview.util.ShortcutKeyMaskExWrapper
- // .getModifiersEx(e)) != 0; // getModifiers()) != 0;
- }
- // answer false for right mouse button
- // shortcut key will be META for a Mac
- return !e.isPopupTrigger()
- && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- & e.getModifiers()) != 0;
- // could we use e.isMetaDown() here?
+ //
+ // System.out.println(e.isPopupTrigger()
+ // + " " + ((SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0)
+ // + " " + e.isControlDown());
+ return (aMac
+ ? !e.isPopupTrigger()
+ && (SHORTCUT_KEY_MASK & e.getModifiersEx()) != 0
+ : e.isControlDown());
}
// BH: I don't know about that previous method. Here is what SwingJS uses.
public static long time, mark, set, duration;
+ /**
+ * typical usage:
+ *
+ * Platform.timeCheck(null, Platform.TIME_MARK);
+ *
+ * ...
+ *
+ * Platform.timeCheck("some message", Platform.TIME_MARK);
+ *
+ * reset...[set/mark]n...get
+ *
+ * @param msg
+ * @param mode
+ */
public static void timeCheck(String msg, int mode)
{
long t = System.currentTimeMillis();
{
case TIME_RESET:
time = mark = t;
+ duration = 0;
if (msg != null)
{
System.err.println("Platform: timer reset\t\t\t" + msg);
case TIME_MARK:
if (set > 0)
{
+ // total time between set/mark points
duration += (t - set);
}
else
public static void cacheFileData(String path, Object data)
{
- if (!isJS() || data == null)
+ if (isJS && data != null)
{
- return;
+ jsutil.cachePathData(path, data);
}
- /**
- * @j2sNative
- *
- * swingjs.JSUtil.cacheFileData$S$O(path, data);
- *
- */
}
public static void cacheFileData(File file)
{
- byte[] data;
- if (!isJS() || (data = Platform.getFileBytes(file)) == null)
+ if (isJS)
{
- return;
+ byte[] data = Platform.getFileBytes(file);
+ {
+ if (data != null)
+ {
+ cacheFileData(file.toString(), data);
+ }
+ }
}
- cacheFileData(file.toString(), data);
}
public static byte[] getFileBytes(File f)
{
- return /** @j2sNative f && swingjs.JSUtil.getFileBytes$java_io_File(f) || */
- null;
+ return (isJS && f != null ? jsutil.getBytes(f) : null);
}
public static byte[] getFileAsBytes(String fileStr)
{
- byte[] bytes = null;
- // BH 2018 hack for no support for access-origin
- /**
- * @j2sNative bytes = swingjs.JSUtil.getFileAsBytes$O(fileStr)
- */
- cacheFileData(fileStr, bytes);
- return bytes;
+ if (isJS && fileStr != null)
+ {
+ byte[] bytes = (byte[]) jsutil.getFile(fileStr, false);
+ cacheFileData(fileStr, bytes);
+ return bytes;
+ }
+ return null;
}
- @SuppressWarnings("unused")
public static String getFileAsString(String url)
{
- String ret = null;
- /**
- * @j2sNative
- *
- * ret = swingjs.JSUtil.getFileAsString$S(url);
- *
- *
- */
- cacheFileData(url, ret);
- return ret;
+ if (isJS && url != null)
+ {
+ String ret = (String) jsutil.getFile(url, true);
+ cacheFileData(url, ret);
+ return ret;
+ }
+ return null;
}
public static boolean setFileBytes(File f, String urlstring)
{
- if (!isJS())
+ if (isJS && f != null && urlstring != null)
{
- return false;
+ @SuppressWarnings("unused")
+ byte[] bytes = getFileAsBytes(urlstring);
+ jsutil.setFileBytes(f, bytes);
+ return true;
}
- @SuppressWarnings("unused")
- byte[] bytes = getFileAsBytes(urlstring);
- // TODO temporary doubling of 秘bytes and _bytes;
- // just remove _bytes when new transpiler has been installed
- /**
- * @j2sNative f.\u79d8bytes = f._bytes = bytes;
- */
- return true;
+ return false;
}
public static void addJ2SBinaryType(String ext)
{
- /**
- * @j2sNative
- *
- * J2S._binaryTypes.push("." + ext + "?");
- *
- */
+ if (isJS)
+ {
+ jsutil.addBinaryFileType(ext);
+ }
}
/**
* @param url
* @return true if window has been opened
*/
- public static boolean openURL(String url)
+ public static boolean openURL(String url) throws IOException
{
if (!isJS())
{
public static String getUniqueAppletID()
{
- /**
- * @j2sNative return swingjs.JSUtil.getApplet$()._uniqueId;
- *
- */
- return null;
-
+ return (isJS ? (String) jsutil.getAppletAttribute("_uniqueId") : null);
}
/**
*/
public static void readInfoProperties(String prefix, Properties p)
{
- if (!isJS())
+ if (isJS)
{
- return;
- }
- String id = getUniqueAppletID();
- String key = "", value = "";
- /**
- * @j2sNative var info = swingjs.JSUtil.getApplet$().__Info || {}; for (var
- * key in info) { if (key.indexOf(prefix) == 0) { value = "" +
- * info[key];
- */
+ String id = getUniqueAppletID();
- System.out.println(
- "Platform id=" + id + " reading Info." + key + " = " + value);
- p.put(id + "_" + key, value);
+ String key = "";
+ String value = "";
+ @SuppressWarnings("unused")
+ Object info = jsutil.getAppletAttribute("__Info");
+ /**
+ * @j2sNative for (key in info) { value = info[key];
+ */
- /**
- * @j2sNative
- *
- *
- * } }
- */
+ if (key.indexOf(prefix) == 0)
+ {
+ System.out.println("Platform id=" + id + " reading Info." + key
+ + " = " + value);
+ p.put(key, value);
+
+ }
+
+ /**
+ * @j2sNative }
+ */
+ }
}
public static void setAjaxJSON(URL url)
public static Object parseJSON(String json) throws ParseException
{
- return (isJS() ? JSON.parse(json)
- : new JSONParser().parse(json));
+ return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
}
public static Object parseJSON(Reader r)
"StringJS does not support FileReader parsing for JSON -- but it could...");
}
return JSON.parse(r);
-
}
/**
* @param is
* @param outFile
* @throws IOException
- * if the file cannot be created or there is a problem
- * reading the input stream.
+ * if the file cannot be created or there is a problem reading the
+ * input stream.
*/
public static void streamToFile(InputStream is, File outFile)
throws IOException
{
- if (isJS() && /**
- * @j2sNative outFile.setBytes$O && outFile.setBytes$O(is) &&
- */
- true)
+
+ if (isJS)
{
+ jsutil.setFileBytes(outFile, is);
return;
}
+
FileOutputStream fio = new FileOutputStream(outFile);
try
{
public static void addJ2SDirectDatabaseCall(String domain)
{
- if (isJS())
+ if (isJS)
{
+ jsutil.addDirectDatabaseCall(domain);
+
System.out.println(
- "Platform adding known access-control-allow-origin * for domain "
- + domain);
- /**
- * @j2sNative
- *
- * J2S.addDirectDatabaseCall(domain);
- */
+ "Platform adding known access-control-allow-origin * for domain "
+ + domain);
}
}
+ /**
+ * Allow for URL-line command arguments. Untested.
+ *
+ */
public static void getURLCommandArguments()
{
- /**
- * Retrieve the first query field as command arguments to Jalview. Include
- * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
- * element to this value.
- *
- * @j2sNative var a =
- * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
- * + "?").split("?")[1].split("#")[0]); a &&
- * (J2S.thisApplet.__Info.args = a.split(" "));
- */
-
+ try
+ {
+ /**
+ * Retrieve the first query field as command arguments to Jalview. Include
+ * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's
+ * __Info.args element to this value.
+ *
+ * @j2sNative var a =
+ * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
+ * + "?").split("?")[1].split("#")[0]); a &&
+ * (J2S.thisApplet.__Info.args = a.split(" "));
+ *
+ * System.out.println("URL arguments: " + a);
+ */
+ } catch (Throwable t)
+ {
+ }
}
/**
- * A (case sensitive) file path comparator that ignores the difference between /
- * and \
+ * A (case sensitive) file path comparator that ignores the difference between
+ * / and \
*
* @param path1
* @param path2
String p2 = path2.replace('\\', '/');
return p1.equals(p2);
}
+
+ ///////////// JAL-3253 Applet additions //////////////
+
+ /**
+ * Retrieve the object's embedded size from a div's style on a page if
+ * embedded in SwingJS.
+ *
+ * @param frame
+ * JFrame or JInternalFrame
+ * @param defaultWidth
+ * use -1 to return null (no default size)
+ * @param defaultHeight
+ * @return the embedded dimensions or null (no default size or not embedded)
+ */
+ public static Dimension getDimIfEmbedded(Component frame,
+ int defaultWidth, int defaultHeight)
+ {
+ Dimension d = null;
+ if (isJS)
+ {
+ d = (Dimension) getEmbeddedAttribute(frame, "dim");
+ }
+ return (d == null && defaultWidth >= 0
+ ? new Dimension(defaultWidth, defaultHeight)
+ : d);
+
+ }
+
+ public static Regex newRegex(String regex)
+ {
+ return newRegex(regex, null);
+ }
+
+ public static Regex newRegex(String searchString, String replaceString)
+ {
+ ensureRegex();
+ return (replaceString == null ? new Regex(searchString)
+ : new Regex(searchString, replaceString));
+ }
+
+ public static Regex newRegexPerl(String code)
+ {
+ ensureRegex();
+ return Regex.perlCode(code);
+ }
+
+ /**
+ * Initialize Java debug logging. A representative sample -- adapt as desired.
+ */
+ public static void startJavaLogging()
+ {
+ /**
+ * @j2sIgnore
+ */
+ {
+ logClass("java.awt.EventDispatchThread", "java.awt.EventQueue",
+ "java.awt.Component", "java.awt.focus.Component",
+ "java.awt.event.Component",
+ "java.awt.focus.DefaultKeyboardFocusManager");
+ }
+ }
+
+ /**
+ * Initiate Java logging for a given class. Only for Java, not JavaScript;
+ * Allows debugging of complex event processing.
+ *
+ * @param className
+ */
+ public static void logClass(String... classNames)
+ {
+ /**
+ * @j2sIgnore
+ *
+ *
+ */
+ {
+ Logger rootLogger = Logger.getLogger("");
+ rootLogger.setLevel(Level.ALL);
+ ConsoleHandler consoleHandler = new ConsoleHandler();
+ consoleHandler.setLevel(Level.ALL);
+ for (int i = classNames.length; --i >= 0;)
+ {
+ Logger logger = Logger.getLogger(classNames[i]);
+ logger.setLevel(Level.ALL);
+ logger.addHandler(consoleHandler);
+ }
+ }
+ }
+
+ /**
+ * load a resource -- probably a core file -- if and only if a particular
+ * class has not been instantialized. We use a String here because if we used
+ * a .class object, that reference itself would simply load the class, and we
+ * want the core package to include that as well.
+ *
+ * @param resourcePath
+ * @param className
+ */
+ public static void loadStaticResource(String resourcePath,
+ String className)
+ {
+ if (isJS)
+ {
+ jsutil.loadResourceIfClassUnknown(resourcePath, className);
+ }
+ }
+
+ public static void ensureRegex()
+ {
+ if (isJS)
+ {
+ loadStaticResource("core/core_stevesoft.z.js",
+ "com.stevesoft.pat.Regex");
+ }
+ }
+
+ /**
+ * Set the "app" property of the HTML5 applet object, for example,
+ * "testApplet.app", to point to the Jalview instance. This will be the object
+ * that page developers use that is similar to the original Java applet object
+ * that was accessed via LiveConnect.
+ *
+ * @param j
+ */
+ public static void setAppClass(Object j)
+ {
+ if (isJS)
+ {
+ jsutil.setAppClass(j);
+ }
+ }
+
+ /**
+ *
+ * If this frame is embedded in a web page, return a known type.
+ *
+ * @param frame
+ * a JFrame or JInternalFrame
+ * @param type
+ * "name", "node", "init", "dim", or any DOM attribute, such as "id"
+ * @return null if frame is not embedded.
+ */
+ public static Object getEmbeddedAttribute(Component frame, String type)
+ {
+ return (isJS ? jsutil.getEmbeddedAttribute(frame, type) : null);
+ }
+
+ public static void stackTrace()
+ {
+ try
+ {
+ throw new NullPointerException();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ }
+
+ public static URL getDocumentBase()
+ {
+ return (isJS ? jsutil.getDocumentBase() : null);
+ }
+
+ public static URL getCodeBase()
+ {
+ return (isJS ? jsutil.getCodeBase() : null);
+ }
+
+ public static String getUserPath(String subpath)
+ {
+ char sep = File.separatorChar;
+ return System.getProperty("user.home") + sep
+ + subpath.replace('/', sep);
+ }
+
+ /**
+ * This method enables checking if a cached file has exceeded a certain
+ * threshold(in days)
+ *
+ * @param file
+ * the cached file
+ * @param noOfDays
+ * the threshold in days
+ * @return
+ */
+ public static boolean isFileOlderThanThreshold(File file, int noOfDays)
+ {
+ if (isJS())
+ {
+ // not meaningful in SwingJS -- this is a session-specific temp file. It
+ // doesn't have a timestamp.
+ return false;
+ }
+ Path filePath = file.toPath();
+ BasicFileAttributes attr;
+ int diffInDays = 0;
+ try
+ {
+ attr = Files.readAttributes(filePath, BasicFileAttributes.class);
+ diffInDays = (int) ((new Date().getTime()
+ - attr.lastModifiedTime().toMillis())
+ / (1000 * 60 * 60 * 24));
+ // System.out.println("Diff in days : " + diffInDays);
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ return noOfDays <= diffInDays;
+ }
+
+ /**
+ * Get the leading integer part of a string that begins with an integer.
+ *
+ * @param input
+ * - the string input to process
+ * @param failValue
+ * - value returned if unsuccessful
+ * @return
+ */
+ public static int getLeadingIntegerValue(String input, int failValue)
+ {
+ if (input == null)
+ {
+ return failValue;
+ }
+ if (isJS)
+ {
+ int val = /** @j2sNative 1 ? parseInt(input) : */
+ 0;
+ return (val == val + 0 ? val : failValue);
+ }
+ // JavaScript does not support Regex ? lookahead
+ String[] parts = input.split("(?=\\D)(?<=\\d)");
+ if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
+ {
+ return Integer.valueOf(parts[0]);
+ }
+ return failValue;
+ }
+
+ public static Map<String, Object> getAppletInfoAsMap()
+ {
+ return (isJS ? jsutil.getAppletInfoAsMap() : null);
+ }
+
+ /**
+ * Get the SwingJS applet ID and combine that with the frameType
+ *
+ * @param frameType
+ * "alignment", "desktop", etc., or null
+ * @return
+ */
+ public static String getAppID(String frameType)
+ {
+
+ String id = Jalview.getInstance().j2sAppletID;
+ if (id == null)
+ {
+ Jalview.getInstance().j2sAppletID = id = (isJS
+ ? (String) jsutil.getAppletAttribute("_id")
+ : "jalview");
+ }
+ return id + (frameType == null ? "" : "-" + frameType);
+ }
+
+ /**
+ * Option to avoid unnecessary seeking of nonexistent resources in JavaScript.
+ * Works in Java as well.
+ *
+ * @param loc
+ * @return
+ */
+ public static Locale getLocaleOrNone(Locale loc)
+ {
+ return (isJS && loc.getLanguage() == "en" ? new Locale("") : loc);
+ }
+
+ /**
+ * From UrlDownloadClient; trivial in JavaScript; painful in Java.
+ *
+ * @param urlstring
+ * @param outfile
+ * @throws IOException
+ */
+ public static void download(String urlstring, String outfile)
+ throws IOException
+ {
+ Path temp = null;
+ try (InputStream is = new URL(urlstring).openStream())
+ {
+ if (isJS)
+ { // so much easier!
+ streamToFile(is, new File(outfile));
+ return;
+ }
+ temp = Files.createTempFile(".jalview_", ".tmp");
+ try (FileOutputStream fos = new FileOutputStream(temp.toString());
+ ReadableByteChannel rbc = Channels.newChannel(is))
+ {
+ fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+ // copy tempfile to outfile once our download completes
+ // incase something goes wrong
+ Files.copy(temp, Paths.get(outfile),
+ StandardCopyOption.REPLACE_EXISTING);
+ }
+ } catch (IOException e)
+ {
+ throw e;
+ } finally
+ {
+ try
+ {
+ if (temp != null)
+ {
+ Files.deleteIfExists(temp);
+ }
+ } catch (IOException e)
+ {
+ System.out.println("Exception while deleting download temp file: "
+ + e.getMessage());
+ }
+ }
+ }
+
}
}
/**
- * Returns the last part of 'input' after the last occurrence of 'token'. For
- * example to extract only the filename from a full path or URL.
- *
- * @param input
- * @param token
- * a delimiter which must be in regular expression format
- * @return
- */
- public static String getLastToken(String input, String token)
- {
- if (input == null)
- {
- return null;
- }
- if (token == null)
- {
- return input;
- }
- String[] st = input.split(token);
- return st[st.length - 1];
- }
-
- /**
* Parses the input string into components separated by the delimiter. Unlike
* String.split(), this method will ignore occurrences of the delimiter which
* are nested within single quotes in name-value pair values, e.g. a='b,c'.
}
return enc;
}
+
+ /**
+ * Answers true if the string is not empty and consists only of digits, or
+ * characters 'a'-'f' or 'A'-'F', else false
+ *
+ * @param s
+ * @return
+ */
+ public static boolean isHexString(String s)
+ {
+ int j = s.length();
+ if (j == 0)
+ {
+ return false;
+ }
+ for (int i = 0; i < j; i++)
+ {
+ int c = s.charAt(i);
+ if (!(c >= '0' && c <= '9' || c >= 'a' && c <= 'f' || c >= 'A' && c <= 'F'))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
}
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignCalcManagerI2;
+import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.util.MessageManager;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
+import jalview.workers.AlignCalcManager2;
import jalview.workers.ComplementConsensusThread;
import jalview.workers.ConsensusThread;
+import jalview.workers.InformationThread;
import jalview.workers.StrucConsensusThread;
import java.awt.Color;
public abstract class AlignmentViewport
implements AlignViewportI, CommandListener, VamsasSource
{
+ public static final String PROPERTY_ALIGNMENT = "alignment";
+ public static final String PROPERTY_SEQUENCE = "sequence";
+
protected ViewportRanges ranges;
protected ViewStyleI viewStyle = new ViewStyle();
* alignment displayed in the viewport. Please use get/setter
*/
protected AlignmentI alignment;
+
+ /*
+ * probably unused indicator that view is of a dataset rather than an
+ * alignment
+ */
+
+ protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
+
+ protected boolean infoLetterHeight = false;
+
+ protected AlignmentAnnotation occupancy;
+
+ /**
+ * results of alignment consensus analysis for visible portion of view
+ */
+ protected ProfilesI consensusProfiles;
+
+ /**
+ * HMM profile for the alignment
+ */
+ protected ProfilesI hmmProfiles;
public AlignmentViewport(AlignmentI al)
{
* alignment
*/
protected boolean isDataset = false;
-
+
public void setDataset(boolean b)
{
isDataset = b;
protected ColumnSelection colSel = new ColumnSelection();
- public boolean autoCalculateConsensus = true;
+ protected boolean autoCalculateConsensusAndConservation = true;
+
+ public boolean getAutoCalculateConsensusAndConservation()
+ { // BH 2019.07.24
+ return autoCalculateConsensusAndConservation;
+ }
+
+ public void setAutoCalculateConsensusAndConservation(boolean b)
+ {
+ autoCalculateConsensusAndConservation = b;
+ }
protected boolean autoCalculateStrucConsensus = true;
+ public boolean getAutoCalculateStrucConsensus()
+ { // BH 2019.07.24
+ return autoCalculateStrucConsensus;
+ }
+
+ public void setAutoCalculateStrucConsensus(boolean b)
+ {
+ autoCalculateStrucConsensus = b;
+ }
+
+
protected boolean ignoreGapsInConsensusCalculation = false;
protected ResidueShaderI residueShading = new ResidueShader();
-
+
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
{
return residueShading;
}
-
+
protected AlignmentAnnotation consensus;
protected AlignmentAnnotation complementConsensus;
protected Hashtable<String, Object>[] hStrucConsensus = null;
protected Conservation hconservation = null;
-
+
@Override
public void setConservation(Conservation cons)
{
}
@Override
+ public void setHmmProfiles(ProfilesI info)
+ {
+ hmmProfiles = info;
+ }
+
+ @Override
+ public ProfilesI getHmmProfiles()
+ {
+ return hmmProfiles;
+ }
+
+ @Override
public Hashtable<String, Object>[] getComplementConsensusHash()
{
return hcomplementConsensus;
return strucConsensus;
}
- protected AlignCalcManagerI calculator = new AlignCalcManager();
+ protected AlignCalcManagerI2 calculator = new AlignCalcManager2();
/**
* trigger update of conservation annotation
// see note in mantis : issue number 8585
if (alignment.isNucleotide()
|| (conservation == null && quality == null)
- || !autoCalculateConsensus)
+ || !autoCalculateConsensusAndConservation)
{
return;
}
- if (calculator.getRegisteredWorkersOfClass(
- jalview.workers.ConservationThread.class) == null)
+ if (calculator.getWorkersOfClass(
+ jalview.workers.ConservationThread.class).isEmpty())
{
calculator.registerWorker(
new jalview.workers.ConservationThread(this, ap));
public void updateConsensus(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if (consensus == null || !autoCalculateConsensus)
+ if (consensus == null || !autoCalculateConsensusAndConservation)
{
return;
}
- if (calculator
- .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
+ if (calculator.getWorkersOfClass(ConsensusThread.class).isEmpty())
{
calculator.registerWorker(new ConsensusThread(this, ap));
}
}
if (doConsensus)
{
- if (calculator.getRegisteredWorkersOfClass(
- ComplementConsensusThread.class) == null)
+ if (calculator.getWorkersOfClass(ComplementConsensusThread.class).isEmpty())
{
- calculator
- .registerWorker(new ComplementConsensusThread(this, ap));
+ calculator.registerWorker(new ComplementConsensusThread(this, ap));
}
}
}
}
+ @Override
+ public void initInformationWorker(final AlignmentViewPanel ap)
+ {
+ if (calculator.getWorkersOfClass(InformationThread.class).isEmpty())
+ {
+ calculator.registerWorker(new InformationThread(this, ap));
+ }
+ }
+
// --------START Structure Conservation
public void updateStrucConsensus(final AlignmentViewPanel ap)
{
{
return;
}
- if (calculator.getRegisteredWorkersOfClass(
- StrucConsensusThread.class) == null)
+ if (calculator.getWorkersOfClass(StrucConsensusThread.class).isEmpty())
{
calculator.registerWorker(new StrucConsensusThread(this, ap));
}
{
return false;
}
- if (calculator.workingInvolvedWith(alignmentAnnotation))
+ if (calculator.isWorkingWithAnnotation(alignmentAnnotation))
{
// System.err.println("grey out ("+alignmentAnnotation.label+")");
return true;
strucConsensus = null;
conservation = null;
quality = null;
+ consensusProfiles = null;
groupConsensus = null;
groupConservation = null;
hconsensus = null;
hconservation = null;
hcomplementConsensus = null;
gapcounts = null;
+ calculator.shutdown();
calculator = null;
residueShading = null; // may hold a reference to Consensus
changeSupport = null;
}
@Override
- public AlignCalcManagerI getCalcManager()
+ public AlignCalcManagerI2 getCalcManager()
{
return calculator;
}
protected boolean showConsensusHistogram = true;
/**
+ * should hmm profile be rendered by default
+ */
+ protected boolean hmmShowSequenceLogo = false;
+
+ /**
+ * should hmm profile be rendered normalised to row height
+ */
+ protected boolean hmmNormaliseSequenceLogo = false;
+
+ /**
+ * should information histograms be rendered by default
+ */
+ protected boolean hmmShowHistogram = true;
+
+ /**
* @return the showConsensusProfile
*/
@Override
}
/**
+ * @return the showInformationProfile
+ */
+ @Override
+ public boolean isShowHMMSequenceLogo()
+ {
+ return hmmShowSequenceLogo;
+ }
+
+ /**
* @param showSequenceLogo
* the new value
*/
// TODO: decouple settings setting from calculation when refactoring
// annotation update method from alignframe to viewport
this.showSequenceLogo = showSequenceLogo;
- calculator.updateAnnotationFor(ConsensusThread.class);
- calculator.updateAnnotationFor(ComplementConsensusThread.class);
- calculator.updateAnnotationFor(StrucConsensusThread.class);
+ for (AlignCalcWorkerI worker : calculator.getWorkers())
+ {
+ if (worker.getClass().equals(ConsensusThread.class) ||
+ worker.getClass().equals(ComplementConsensusThread.class) ||
+ worker.getClass().equals(StrucConsensusThread.class))
+ {
+ worker.updateAnnotation();
+ }
+ }
}
this.showSequenceLogo = showSequenceLogo;
}
+ public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo)
+ {
+ if (showHMMSequenceLogo != this.hmmShowSequenceLogo)
+ {
+ this.hmmShowSequenceLogo = showHMMSequenceLogo;
+ // TODO: updateAnnotation if description (tooltip) will show
+ // profile in place of information content?
+ // calculator.updateAnnotationFor(InformationThread.class);
+ }
+ this.hmmShowSequenceLogo = showHMMSequenceLogo;
+ }
+
/**
* @param showConsensusHistogram
* the showConsensusHistogram to set
}
/**
+ * @param showInformationHistogram
+ */
+ public void setShowInformationHistogram(boolean showInformationHistogram)
+ {
+ this.hmmShowHistogram = showInformationHistogram;
+ }
+
+ /**
* @return the showGroupConservation
*/
public boolean isShowGroupConservation()
}
/**
+ *
+ * @return flag to indicate if the information content histogram should be
+ * rendered by default
+ */
+ @Override
+ public boolean isShowInformationHistogram()
+ {
+ return this.hmmShowHistogram;
+ }
+
+ /**
* when set, updateAlignment will always ensure sequences are of equal length
*/
private boolean padGaps = false;
ignoreGapsInConsensusCalculation);
}
}
+ }
+
+ public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap)
+ {
+ ignoreBelowBackGroundFrequencyCalculation = b;
+ }
+ public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap)
+ {
+ infoLetterHeight = b;
}
private long sgrouphash = -1, colselhash = -1;
* checks current colsel against record of last hash value, and optionally
* updates record.
*
- * @param b
+ * @param updateHash
* update the record of last hash value
* @return true if colsel changed since last call (when b is true)
*/
- public boolean isColSelChanged(boolean b)
+ public boolean isColSelChanged(boolean updateHash)
{
int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
if (hc != -1 && hc != colselhash)
{
- if (b)
+ if (updateHash)
{
colselhash = hc;
}
return true;
}
+ notifySequence();
return false;
}
return ignoreGapsInConsensusCalculation;
}
+ @Override
+ public boolean isIgnoreBelowBackground()
+ {
+ return ignoreBelowBackGroundFrequencyCalculation;
+ }
+
+ @Override
+ public boolean isInfoLetterHeight()
+ {
+ return infoLetterHeight;
+ }
+
// property change stuff
// JBPNote Prolly only need this in the applet version.
private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
}
}
- /**
- * Property change listener for changes in alignment
- *
- * @param prop
- * DOCUMENT ME!
- * @param oldvalue
- * DOCUMENT ME!
- * @param newvalue
- * DOCUMENT ME!
- */
- public void firePropertyChange(String prop, Object oldvalue,
- Object newvalue)
- {
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);
- }
-
// common hide/show column stuff
public void hideSelectedColumns()
ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
- firePropertyChange("alignment", null, alignment.getSequences());
// used to set hasHiddenRows/hiddenRepSequences here, after the property
// changed event
+ notifySequence();
sendSelection();
}
}
+
public void showSequence(int index)
{
int startSeq = ranges.getStartSeq();
}
ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
-
- firePropertyChange("alignment", null, alignment.getSequences());
+ notifyAlignment();
sendSelection();
}
}
setSequenceAnnotationsVisible(seq[i], false);
}
ranges.setStartSeq(startSeq);
- firePropertyChange("alignment", null, alignment.getSequences());
+ notifyAlignment();
}
}
{
alignment.padGaps();
}
- if (autoCalculateConsensus)
+ if (autoCalculateConsensusAndConservation)
{
updateConsensus(ap);
}
- if (hconsensus != null && autoCalculateConsensus)
+ if (hconsensus != null && autoCalculateConsensusAndConservation)
{
updateConservation(ap);
}
updateAllColourSchemes();
calculator.restartWorkers();
- // alignment.adjustSequenceAnnotations();
}
/**
MessageManager.getString("label.consensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
+
initGapCounts();
initComplementConsensus();
boolean showprf = isShowSequenceLogo();
boolean showConsHist = isShowConsensusHistogram();
boolean normLogo = isNormaliseSequenceLogo();
+ boolean showHMMPrf = isShowHMMSequenceLogo();
+ boolean showInfoHist = isShowInformationHistogram();
+ boolean normHMMLogo = isNormaliseHMMSequenceLogo();
/**
* TODO reorder the annotation rows according to group/sequence ordering on
sg.setshowSequenceLogo(showprf);
sg.setShowConsensusHistogram(showConsHist);
sg.setNormaliseSequenceLogo(normLogo);
+ sg.setShowHMMSequenceLogo(showHMMPrf);
+ sg.setShowInformationHistogram(showInfoHist);
+ sg.setNormaliseHMMSequenceLogo(normHMMLogo);
}
if (conv)
{
return sq;
}
+ public boolean hasReferenceAnnotation()
+ {
+ AlignmentAnnotation[] annots = this.alignment.getAlignmentAnnotation();
+ for (AlignmentAnnotation annot : annots)
+ {
+ if ("RF".equals(annot.label) || annot.label.contains("Reference"))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
@Override
public void setCurrentTree(TreeModel tree)
{
return ed;
}
+ @Override
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ public void setNormaliseSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
+ @Override
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ return hmmNormaliseSequenceLogo;
+ }
+
+ public void setNormaliseHMMSequenceLogo(boolean state)
+ {
+ hmmNormaliseSequenceLogo = state;
+ }
/**
* flag set to indicate if structure views might be out of sync with sequences
* in the alignment
codingComplement.setUpdateStructures(needToUpdateStructureViews);
}
}
-
-
+ /**
+ * Filters out sequences with an eValue higher than the specified value. The
+ * filtered sequences are hidden or deleted. Sequences with no eValues are also
+ * filtered out.
+ *
+ * @param eValue
+ * @param delete
+ */
+ public void filterByEvalue(double eValue)
+ {
+ for (SequenceI seq : alignment.getSequencesArray())
+ {
+ if ((seq.getAnnotation("Search Scores") == null
+ || seq.getAnnotation("Search Scores")[0].getEValue() > eValue)
+ && seq.getHMM() == null)
+ {
+ hideSequence(new SequenceI[] { seq });
+ }
+ }
+ }
+
+ /**
+ * Filters out sequences with an score lower than the specified value. The
+ * filtered sequences are hidden or deleted.
+ *
+ * @param score
+ * @param delete
+ */
+ public void filterByScore(double score)
+ {
+ for (SequenceI seq : alignment.getSequencesArray())
+ {
+ if ((seq.getAnnotation("Search Scores") == null
+ || seq.getAnnotation("Search Scores")[0]
+ .getBitScore() < score)
+ && seq.getHMM() == null)
+ {
+ hideSequence(new SequenceI[] { seq });
+ }
+ }
++ }
+
+ /**
+ * Notify TreePanel and AlignmentPanel of some sort of alignment change.
+ */
+ public void notifyAlignment()
+ {
+ changeSupport.firePropertyChange(PROPERTY_ALIGNMENT, null, alignment.getSequences());
+ }
+
+ /**
+ * Notify AlignmentPanel of a sequence column selection or visibility changes.
+ */
+ public void notifySequence()
+ {
+ changeSupport.firePropertyChange(PROPERTY_SEQUENCE, null, null);
}
-
}
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignCalcWorkerI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import java.util.ArrayList;
import java.util.Collections;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
/*
* list of registered workers
*/
- private volatile List<AlignCalcWorkerI> restartable;
+ private final List<AlignCalcWorkerI> restartable = Collections
+ .synchronizedList(new ArrayList<AlignCalcWorkerI>());
/*
* types of worker _not_ to run (for example, because they have
* previously thrown errors)
*/
- private volatile List<Class<? extends AlignCalcWorkerI>> blackList;
+ private final List<Class<? extends AlignCalcWorkerI>> blackList = Collections
+ .synchronizedList(new ArrayList<Class<? extends AlignCalcWorkerI>>());
/*
* global record of calculations in progress
*/
- private volatile List<AlignCalcWorkerI> inProgress;
+ private final List<AlignCalcWorkerI> inProgress = Collections
+ .synchronizedList(new ArrayList<AlignCalcWorkerI>());
/*
* record of calculations pending or in progress in the current context
*/
- private volatile Map<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>> updating;
+ private final Map<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>> updating =
+ new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>();
/*
* workers that have run to completion so are candidates for visual-only
* update of their results
*/
- private HashSet<AlignCalcWorkerI> canUpdate;
+ private HashSet<AlignCalcWorkerI> canUpdate = new HashSet<>();;
- /**
- * Constructor
- */
- public AlignCalcManager()
+ private static boolean listContains(List<AlignCalcWorkerI> upd,
+ AlignCalcWorkerI worker)
{
- restartable = Collections
- .synchronizedList(new ArrayList<AlignCalcWorkerI>());
- blackList = Collections.synchronizedList(
- new ArrayList<Class<? extends AlignCalcWorkerI>>());
- inProgress = Collections
- .synchronizedList(new ArrayList<AlignCalcWorkerI>());
- updating = Collections.synchronizedMap(
- new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
- canUpdate = new HashSet<AlignCalcWorkerI>();
+ // avoid use of 'Contains' in case
+ for (AlignCalcWorkerI _otherworker : upd)
+ {
+ if (_otherworker == upd)
+ {
+ return true;
+ }
+ }
+ return false;
}
-
@Override
- public void notifyStart(AlignCalcWorkerI worker)
+ public void notifyStarted(AlignCalcWorkerI worker)
{
synchronized (updating)
{
}
synchronized (upd)
{
- upd.add(worker);
+ if (listContains(upd, worker))
+ {
+ Cache.log.debug(
+ "Ignoring second call to notifyStart for worker "
+ + worker);
+ }
+ else
+ {
+ upd.add(worker);
+ }
}
}
}
@Override
public boolean isPending(AlignCalcWorkerI workingClass)
{
- List<AlignCalcWorkerI> upd;
synchronized (updating)
{
- upd = updating.get(workingClass.getClass());
- if (upd == null)
- {
- return false;
- }
- synchronized (upd)
- {
- if (upd.size() > 1)
- {
- return true;
- }
- }
- return false;
+ List<AlignCalcWorkerI> upd = updating.get(workingClass.getClass());
+ return upd != null && upd.size() > 1;
}
}
{
synchronized (inProgress)
{
- if (inProgress.contains(worker))
+ if (listContains(inProgress, worker))
{
return false; // worker is already working, so ask caller to wait around
}
{
synchronized (inProgress)
{
- // System.err.println("Worker " + worker + " marked as complete.");
+ Cache.log.debug("Worker " + worker + " marked as complete.");
inProgress.remove(worker);
List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
if (upd != null)
{
if (!isDisabled(worker))
{
- Thread tw = new Thread(worker);
+ Thread tw = new Thread(() -> {
+ try
+ {
+ worker.run();
+ } catch (Throwable e)
+ {
+ e.printStackTrace();
+ }
+ });
tw.setName(worker.getClass().toString());
tw.start();
}
}
}
+ public int getQueueLength() {
+ return inProgress.size();
+ }
+
@Override
public void registerWorker(AlignCalcWorkerI worker)
{
synchronized (restartable)
{
- if (!restartable.contains(worker))
+ if (!listContains(restartable, worker))
{
restartable.add(worker);
}
public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
Class<? extends AlignCalcWorkerI> workerClass)
{
- List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
+ List<AlignCalcWorkerI> workingClass = new ArrayList<>();
synchronized (canUpdate)
{
for (AlignCalcWorkerI worker : canUpdate)
}
@Override
- public void removeRegisteredWorkersOfClass(
+ public void removeWorkersOfClass(
Class<? extends AlignCalcWorkerI> typeToRemove)
{
- List<AlignCalcWorkerI> removable = new ArrayList<AlignCalcWorkerI>();
- Set<AlignCalcWorkerI> toremovannot = new HashSet<AlignCalcWorkerI>();
+ List<AlignCalcWorkerI> removable = new ArrayList<>();
+ Set<AlignCalcWorkerI> toremovannot = new HashSet<>();
synchronized (restartable)
{
for (AlignCalcWorkerI worker : restartable)
* first just find those to remove (to avoid
* ConcurrentModificationException)
*/
- List<AlignCalcWorkerI> toRemove = new ArrayList<AlignCalcWorkerI>();
+ List<AlignCalcWorkerI> toRemove = new ArrayList<>();
for (AlignCalcWorkerI worker : restartable)
{
if (worker.involves(ann))
*/
package jalview.ws.jws1;
- import jalview.bin.Cache;
- import jalview.gui.JvOptionPane;
- import jalview.util.MessageManager;
-
import java.net.URL;
import java.util.Hashtable;
import java.util.StringTokenizer;
import ext.vamsas.RegistryServiceSoapBindingStub;
import ext.vamsas.ServiceHandle;
import ext.vamsas.ServiceHandles;
++import jalview.bin.Cache;
+ import jalview.bin.ApplicationSingletonProvider;
+ import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+ import jalview.gui.JvOptionPane;
+ import jalview.util.MessageManager;
- public class Discoverer implements Runnable
+ public class Discoverer implements Runnable, ApplicationSingletonI
{
+
+ public static Discoverer getInstance()
+ {
+ return (Discoverer) ApplicationSingletonProvider.getInstance(Discoverer.class);
+ }
+
+ private Discoverer()
+ {
+ // use getInstance()
+ }
+
ext.vamsas.IRegistry registry; // the root registry service.
private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
return server;
}
- static private java.net.URL RootServiceURL = null;
+ private java.net.URL RootServiceURL = null;
- static public Vector<URL> ServiceURLList = null;
+ private Vector<URL> ServiceURLList = null;
- static private boolean reallyDiscoverServices = true;
+ public Vector<URL> getServiceURLList() {
+ return ServiceURLList;
+ }
+
+ private boolean reallyDiscoverServices = true;
- public static java.util.Hashtable<String, Vector<ServiceHandle>> services = null;
+ private java.util.Hashtable<String, Vector<ServiceHandle>> services = null;
// stored by
// abstractServiceType
// string
- public static java.util.Vector<ServiceHandle> serviceList = null;
+ public java.util.Vector<ServiceHandle> serviceList = null;
- static private Vector<URL> getDiscoveryURLS()
+ private Vector<URL> getDiscoveryURLS()
{
Vector<URL> urls = new Vector<>();
String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
*/
static public void doDiscovery()
{
+ getInstance().discovery();
+ }
+
+ private void discovery()
+ {
jalview.bin.Cache.log
.debug("(Re)-Initialising the discovery URL list.");
try
{
+ Discoverer d = getInstance();
reallyDiscoverServices = jalview.bin.Cache
.getDefault("DISCOVERY_START", false);
if (reallyDiscoverServices)
// JBPNote - should do this a better way!
if (f.getFaultReason().indexOf("(407)") > -1)
{
- if (jalview.gui.Desktop.desktop != null)
+ if (jalview.gui.Desktop.getDesktopPane() != null)
{
- JvOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
+ JvOptionPane.showMessageDialog(jalview.gui.Desktop.getDesktopPane(),
MessageManager.getString("label.set_proxy_settings"),
MessageManager
.getString("label.proxy_authorization_failed"),
* Hashtable
* @return boolean
*/
- static private boolean buildServiceLists(ServiceHandle[] sh,
+ private boolean buildServiceLists(ServiceHandle[] sh,
Vector<ServiceHandle> cat,
Hashtable<String, Vector<ServiceHandle>> sscat)
{
@Override
public void run()
{
- final Discoverer discoverer = this;
- Thread discoverThread = new Thread()
- {
- @Override
- public void run()
- {
- Discoverer.doDiscovery();
- discoverer.discoverServices();
- }
- };
- discoverThread.start();
+ Cache.log.info("Discovering jws1 services");
+ Discoverer.doDiscovery();
+ discoverServices();
}
/**
* binding service abstract name to handler class
*/
- private static Hashtable<String, WS1Client> serviceClientBindings;
+ private Hashtable<String, WS1Client> serviceClientBindings;
public static WS1Client getServiceClient(ServiceHandle sh)
{
+ return getInstance().getClient(sh);
+ }
+
+ /**
+ * notes on discovery service 1. need to allow multiple discovery source urls.
+ * 2. user interface to add/control list of urls in preferences notes on
+ * wsclient discovery 1. need a classpath property with list of additional
+ * plugin directories 2. optional config to cite specific bindings between
+ * class name and Abstract service name. 3. precedence for automatic discovery
+ * by using getAbstractName for WSClient - user added plugins override default
+ * plugins ? notes on wsclient gui code for gui attachment now moved to
+ * wsclient implementation. Needs more abstraction but approach seems to work.
+ * is it possible to 'generalise' the data retrieval calls further ? current
+ * methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred),
+ * new methods for conservation (group or alignment), treecalc (aligned
+ * profile), seqannot (sequences selected from dataset, annotation back to
+ * dataset).
+ *
+ */
+
+ private WS1Client getClient(ServiceHandle sh)
+ {
if (serviceClientBindings == null)
{
// get a list from Config or create below
}
return instance;
}
- /**
- * notes on discovery service 1. need to allow multiple discovery source urls.
- * 2. user interface to add/control list of urls in preferences notes on
- * wsclient discovery 1. need a classpath property with list of additional
- * plugin directories 2. optional config to cite specific bindings between
- * class name and Abstract service name. 3. precedence for automatic discovery
- * by using getAbstractName for WSClient - user added plugins override default
- * plugins ? notes on wsclient gui code for gui attachment now moved to
- * wsclient implementation. Needs more abstraction but approach seems to work.
- * is it possible to 'generalise' the data retrieval calls further ? current
- * methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred),
- * new methods for conservation (group or alignment), treecalc (aligned
- * profile), seqannot (sequences selected from dataset, annotation back to
- * dataset).
- *
- */
+
+ public static Hashtable<String, Vector<ServiceHandle>> getServices()
+ {
+ return getInstance().services;
+ }
}
*/
ext.vamsas.MuscleWS server;
- AlignFrame alignFrame;
-
/**
* Creates a new MsaWSClient object that uses a service given by an externally
* retrieved ServiceHandle
alignFrame = _alignFrame;
if (!sh.getAbstractName().equals("MsaWS"))
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.service_called_is_not_msa_service",
new String[]
if ((wsInfo = setWebService(sh)) == null)
{
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager
.formatMessage("label.msa_service_is_unknown", new String[]
{ sh.getName() }),
MessageManager.getString("label.internal_jalview_error"),
*/
ext.vamsas.SeqSearchI server;
- AlignFrame alignFrame;
-
/**
* Creates a new MsaWSClient object that uses a service given by an externally
* retrieved ServiceHandle
// name to service client name
if (!sh.getAbstractName().equals(this.getServiceActionKey()))
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.service_called_is_not_seq_search_service",
new String[]
if ((wsInfo = setWebService(sh)) == null)
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.seq_search_service_is_unknown", new String[]
{ sh.getName() }),
--- /dev/null
+package jalview.ws.jws2;
+
+import jalview.gui.WsJobParameters;
+import jalview.util.MessageManager;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+
+import java.awt.BorderLayout;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+import compbio.metadata.Option;
+import compbio.metadata.Parameter;
+import compbio.metadata.Preset;
+import compbio.metadata.PresetManager;
+
+public class JabaWsParamTest
+{
+
+ /**
+ * testing method - grab a service and parameter set and show the window
+ *
+ * @param args
+ */
+ public static void main(String[] args)
+ {
+ jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
- .getDiscoverer();
++ .getInstance();
+ int p = 0;
+ if (args.length > 0)
+ {
+ Vector<String> services = new Vector<>();
+ services.addElement(args[p++]);
- Jws2Discoverer.getDiscoverer().setServiceUrls(services);
++ Jws2Discoverer.getInstance().setServiceUrls(services);
+ }
+ try
+ {
+ disc.run();
+ } catch (Exception e)
+ {
+ System.err.println("Aborting. Problem discovering services.");
+ e.printStackTrace();
+ return;
+ }
+ Jws2Instance lastserv = null;
+ for (ServiceWithParameters service : disc.getServices())
+ {
+ // this will fail for non-JABAWS services !
+ lastserv = (Jws2Instance) service;
+ if (p >= args.length || service.getName().equalsIgnoreCase(args[p]))
+ {
+ if (lastserv != null)
+ {
+ List<Preset> prl = null;
+ Preset pr = null;
+ if (++p < args.length)
+ {
+ PresetManager prman = lastserv.getPresets();
+ if (prman != null)
+ {
+ pr = prman.getPresetByName(args[p]);
+ if (pr == null)
+ {
+ // just grab the last preset.
+ prl = prman.getPresets();
+ }
+ }
+ }
+ else
+ {
+ PresetManager prman = lastserv.getPresets();
+ if (prman != null)
+ {
+ prl = prman.getPresets();
+ }
+ }
+ Iterator<Preset> en = (prl == null) ? null : prl.iterator();
+ while (en != null && en.hasNext())
+ {
+ if (en != null)
+ {
+ if (!en.hasNext())
+ {
+ en = prl.iterator();
+ }
+ pr = en.next();
+ }
+ {
+ System.out.println("Testing opts dupes for "
+ + lastserv.getUri() + " : " + lastserv.getActionText()
+ + ":" + pr.getName());
+ List<Option> rg = lastserv.getRunnerConfig().getOptions();
+ for (Option o : rg)
+ {
+ try
+ {
+ Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
+ } catch (Exception e)
+ {
+ System.err.println("Failed to copy " + o.getName());
+ e.printStackTrace();
+ } catch (Error e)
+ {
+ System.err.println("Failed to copy " + o.getName());
+ e.printStackTrace();
+ }
+ }
+ }
+ {
+ System.out.println("Testing param dupes:");
+ List<Parameter> rg = lastserv.getRunnerConfig()
+ .getParameters();
+ for (Parameter o : rg)
+ {
+ try
+ {
+ Parameter cpy = jalview.ws.jws2.ParameterUtils
+ .copyParameter(o);
+ } catch (Exception e)
+ {
+ System.err.println("Failed to copy " + o.getName());
+ e.printStackTrace();
+ } catch (Error e)
+ {
+ System.err.println("Failed to copy " + o.getName());
+ e.printStackTrace();
+ }
+ }
+ }
+ {
+ System.out.println("Testing param write:");
+ List<String> writeparam = null, readparam = null;
+ try
+ {
+ writeparam = jalview.ws.jws2.ParameterUtils
+ .writeParameterSet(
+ pr.getArguments(lastserv.getRunnerConfig()),
+ " ");
+ System.out.println("Testing param read :");
+ List<Option> pset = jalview.ws.jws2.ParameterUtils
+ .processParameters(writeparam,
+ lastserv.getRunnerConfig(), " ");
+ readparam = jalview.ws.jws2.ParameterUtils
+ .writeParameterSet(pset, " ");
+ Iterator<String> o = pr.getOptions().iterator(),
+ s = writeparam.iterator(), t = readparam.iterator();
+ boolean failed = false;
+ while (s.hasNext() && t.hasNext())
+ {
+ String on = o.next(), sn = s.next(), st = t.next();
+ if (!sn.equals(st))
+ {
+ System.out.println(
+ "Original was " + on + " Phase 1 wrote " + sn
+ + "\tPhase 2 wrote " + st);
+ failed = true;
+ }
+ }
+ if (failed)
+ {
+ System.out.println(
+ "Original parameters:\n" + pr.getOptions());
+ System.out.println(
+ "Wrote parameters in first set:\n" + writeparam);
+ System.out.println(
+ "Wrote parameters in second set:\n" + readparam);
+
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ WsJobParameters pgui = new WsJobParameters(null, lastserv,
+ new JabaPreset(lastserv, pr), null);
+ JFrame jf = new JFrame(MessageManager
+ .formatMessage("label.ws_parameters_for", new String[]
+ { lastserv.getActionText() }));
+ JPanel cont = new JPanel(new BorderLayout());
+ pgui.validate();
+ cont.setPreferredSize(pgui.getPreferredSize());
+ cont.add(pgui, BorderLayout.CENTER);
+ jf.setLayout(new BorderLayout());
+ jf.add(cont, BorderLayout.CENTER);
+ jf.validate();
+ final Thread thr = Thread.currentThread();
+ jf.addWindowListener(new WindowListener()
+ {
+
+ @Override
+ public void windowActivated(WindowEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void windowClosed(WindowEvent e)
+ {
+ }
+
+ @Override
+ public void windowClosing(WindowEvent e)
+ {
+ thr.interrupt();
+
+ }
+
+ @Override
+ public void windowDeactivated(WindowEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void windowDeiconified(WindowEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void windowIconified(WindowEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void windowOpened(WindowEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ });
+ jf.setVisible(true);
+ boolean inter = false;
+ while (!inter)
+ {
+ try
+ {
+ Thread.sleep(10000);
+ } catch (Exception e)
+ {
+ inter = true;
+ }
+ ;
+ }
+ jf.dispose();
+ }
+ }
+ }
+ }
+ }
+
+}
package jalview.ws.jws2;
import jalview.bin.Cache;
+ import jalview.bin.ApplicationSingletonProvider;
+ import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
-import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.ServiceChangeListener;
+import jalview.ws.WSDiscovererI;
+import jalview.ws.api.ServiceWithParameters;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ParamDatastoreI;
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.beans.PropertyChangeSupport;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
+import java.util.Collections;
import java.util.HashSet;
-import java.util.Hashtable;
import java.util.List;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.Vector;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.CopyOnWriteArraySet;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.Future;
+import java.util.concurrent.FutureTask;
import javax.swing.JMenu;
-import javax.swing.JMenuItem;
import compbio.ws.client.Services;
* @author JimP
*
*/
- public class Jws2Discoverer implements WSDiscovererI, Runnable
-public class Jws2Discoverer
- implements Runnable, WSMenuEntryProviderI, ApplicationSingletonI
++public class Jws2Discoverer implements WSDiscovererI, Runnable, ApplicationSingletonI
{
+
+ /**
+ * Returns the singleton instance of this class.
+ *
+ * @return
+ */
+ public static Jws2Discoverer getInstance()
+ {
+ return (Jws2Discoverer) ApplicationSingletonProvider
+ .getInstance(Jws2Discoverer.class);
+ }
+
- /**
- * Private constructor enforces use of singleton via getDiscoverer()
- */
- private Jws2Discoverer()
- {
- // use getInstance();
- }
-
public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws";
/*
private final static String JWS2HOSTURLS = "JWS2HOSTURLS";
/*
- * Singleton instance
- */
- private static Jws2Discoverer discoverer;
-
- /*
* Override for testing only
*/
- private static List<String> testUrls = null;
+ private List<String> testUrls = null;
// preferred url has precedence over others
private String preferredUrl;
-
- protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
- this);
-
+
+ private Set<ServiceChangeListener> serviceListeners = new CopyOnWriteArraySet<>();
-
private Vector<String> invalidServiceUrls = null;
private Vector<String> urlsWithoutServices = null;
private volatile boolean running = false;
private volatile boolean aborted = false;
-
- private Thread oldthread = null;
+
+ private volatile Thread oldthread = null;
/**
* holds list of services.
protected Vector<Jws2Instance> services;
/**
- * change listeners are notified of "services" property changes
- *
- * @param listener
- * to be added that consumes new services Hashtable object.
+ * Private constructor enforces use of singleton via getDiscoverer()
*/
- public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ private Jws2Discoverer()
{
- changeSupport.addPropertyChangeListener(listener);
}
- /**
- *
- *
- * @param listener
- * to be removed
- */
- public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+
+ @Override
+ public void addServiceChangeListener(ServiceChangeListener listener)
+ {
+ serviceListeners.add(listener);
+ }
+
+ @Override
+ public void removeServiceChangeListener(ServiceChangeListener listener)
{
- changeSupport.removePropertyChangeListener(listener);
+ serviceListeners.remove(listener);
+ }
+
+ private void notifyServiceListeners(List<? extends ServiceWithParameters> services)
+ {
+ if (services == null) services = this.services;
+ for (var listener : serviceListeners) {
+ listener.servicesChanged(this, services);
+ }
}
/**
ignoredServices.add(ignored);
}
- changeSupport.firePropertyChange("services", services,
- new Vector<Jws2Instance>());
+ notifyServiceListeners(Collections.emptyList());
oldthread = Thread.currentThread();
try
{
- getClass().getClassLoader()
- .loadClass("compbio.ws.client.Jws2Client");
+ getClass().getClassLoader().loadClass("compbio.ws.client.Jws2Client");
} catch (ClassNotFoundException e)
{
System.err.println(
for (Jws2Instance svc : services)
{
svcs[ipos] = svc;
- spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHost()) + 1
- + svctypes.indexOf(svc.serviceType);
+ spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHostURL()) + 1
+ + svctypes.indexOf(svc.getName());
}
jalview.util.QuickSort.sort(spos, svcs);
services = new Vector<>();
for (Jws2Instance svc : svcs)
{
- if (!ignoredServices.contains(svc.serviceType))
+ if (!ignoredServices.contains(svc.getName()))
{
services.add(svc);
}
}
oldthread = null;
running = false;
- changeSupport.firePropertyChange("services", new Vector<Jws2Instance>(),
- services);
+ notifyServiceListeners(services);
}
/**
}
/**
- * attach all available web services to the appropriate submenu in the given
- * JMenu
- */
- @Override
- public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
- {
- // dynamically regenerate service list.
- populateWSMenuEntry(wsmenu, alignFrame, null);
- }
-
- private boolean isRecalculable(String action)
- {
- return (action != null && action.equalsIgnoreCase("conservation"));
- }
-
- private void populateWSMenuEntry(JMenu jws2al,
- final AlignFrame alignFrame, String typeFilter)
- {
- if (running || services == null || services.size() == 0)
- {
- return;
- }
-
- /**
- * eventually, JWS2 services will appear under the same align/etc submenus.
- * for moment we keep them separate.
- */
- JMenu atpoint;
- List<Jws2Instance> enumerableServices = new ArrayList<>();
- // jws2al.removeAll();
- Map<String, Jws2Instance> preferredHosts = new HashMap<>();
- Map<String, List<Jws2Instance>> alternates = new HashMap<>();
- for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
- {
- if (!isRecalculable(service.action))
- {
- // add 'one shot' services to be displayed using the classic menu
- // structure
- enumerableServices.add(service);
- }
- else
- {
- if (!preferredHosts.containsKey(service.serviceType))
- {
- Jws2Instance preferredInstance = getPreferredServiceFor(
- alignFrame, service.serviceType);
- if (preferredInstance != null)
- {
- preferredHosts.put(service.serviceType, preferredInstance);
- }
- else
- {
- preferredHosts.put(service.serviceType, service);
- }
- }
- List<Jws2Instance> ph = alternates.get(service.serviceType);
- if (preferredHosts.get(service.serviceType) != service)
- {
- if (ph == null)
- {
- ph = new ArrayList<>();
- }
- ph.add(service);
- alternates.put(service.serviceType, ph);
- }
- }
-
- }
-
- // create GUI element for classic services
- addEnumeratedServices(jws2al, alignFrame, enumerableServices);
- // and the instantaneous services
- for (final Jws2Instance service : preferredHosts.values())
- {
- atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
- JMenuItem hitm;
- if (atpoint.getItemCount() > 1)
- {
- // previous service of this type already present
- atpoint.addSeparator();
- }
- atpoint.add(hitm = new JMenuItem(service.getHost()));
- hitm.setForeground(Color.blue);
- hitm.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- Desktop.showUrl(service.getHost());
- }
- });
- hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
- MessageManager.getString("label.open_jabaws_web_page")));
-
- service.attachWSMenuEntry(atpoint, alignFrame);
- if (alternates.containsKey(service.serviceType))
- {
- atpoint.add(hitm = new JMenu(
- MessageManager.getString("label.switch_server")));
- hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
- MessageManager.getString("label.choose_jabaws_server")));
- for (final Jws2Instance sv : alternates.get(service.serviceType))
- {
- JMenuItem itm;
- hitm.add(itm = new JMenuItem(sv.getHost()));
- itm.setForeground(Color.blue);
- itm.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- setPreferredServiceFor(alignFrame, sv.serviceType,
- sv.action, sv);
- changeSupport.firePropertyChange("services",
- new Vector<Jws2Instance>(), services);
- }
- }).start();
-
- }
- });
- }
- }
- }
- }
-
- /**
- * add services using the Java 2.5/2.6/2.7 system which optionally creates
- * submenus to index by host and service program type
- */
- private void addEnumeratedServices(final JMenu jws2al,
- final AlignFrame alignFrame,
- List<Jws2Instance> enumerableServices)
- {
- boolean byhost = Cache.getDefault("WSMENU_BYHOST", false),
- bytype = Cache.getDefault("WSMENU_BYTYPE", false);
- /**
- * eventually, JWS2 services will appear under the same align/etc submenus.
- * for moment we keep them separate.
- */
- JMenu atpoint;
-
- List<String> hostLabels = new ArrayList<>();
- Hashtable<String, String> lasthostFor = new Hashtable<>();
- Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<>();
- ArrayList<String> hostlist = new ArrayList<>();
- for (Jws2Instance service : enumerableServices)
- {
- ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
- if (hostservices == null)
- {
- hosts.put(service.getHost(),
- hostservices = new ArrayList<>());
- hostlist.add(service.getHost());
- }
- hostservices.add(service);
- }
- // now add hosts in order of the given array
- for (String host : hostlist)
- {
- Jws2Instance orderedsvcs[] = hosts.get(host)
- .toArray(new Jws2Instance[1]);
- String sortbytype[] = new String[orderedsvcs.length];
- for (int i = 0; i < sortbytype.length; i++)
- {
- sortbytype[i] = orderedsvcs[i].serviceType;
- }
- jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
- for (final Jws2Instance service : orderedsvcs)
- {
- atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action);
- String type = service.serviceType;
- if (byhost)
- {
- atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
- if (atpoint.getToolTipText() == null)
- {
- atpoint.setToolTipText(MessageManager
- .formatMessage("label.services_at", new String[]
- { host }));
- }
- }
- if (bytype)
- {
- atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type);
- if (atpoint.getToolTipText() == null)
- {
- atpoint.setToolTipText(service.getActionText());
- }
- }
- if (!byhost && !hostLabels.contains(
- host + service.serviceType + service.getActionText()))
- // !hostLabels.contains(host + (bytype ?
- // service.serviceType+service.getActionText() : "")))
- {
- // add a marker indicating where this service is hosted
- // relies on services from the same host being listed in a
- // contiguous
- // group
- JMenuItem hitm;
- if (hostLabels.contains(host))
- {
- atpoint.addSeparator();
- }
- else
- {
- hostLabels.add(host);
- }
- if (lasthostFor.get(service.action) == null
- || !lasthostFor.get(service.action).equals(host))
- {
- atpoint.add(hitm = new JMenuItem(host));
- hitm.setForeground(Color.blue);
- hitm.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- Desktop.showUrl(service.getHost());
- }
- });
- hitm.setToolTipText(
- JvSwingUtils.wrapTooltip(true, MessageManager
- .getString("label.open_jabaws_web_page")));
- lasthostFor.put(service.action, host);
- }
- hostLabels.add(
- host + service.serviceType + service.getActionText());
- }
-
- service.attachWSMenuEntry(atpoint, alignFrame);
- }
- }
- }
-
- /**
*
* @param args
* @j2sIgnore
*/
public static void main(String[] args)
{
+ Jws2Discoverer instance = getInstance();
if (args.length > 0)
{
- testUrls = new ArrayList<>();
+ instance.testUrls = new ArrayList<>();
for (String url : args)
{
- testUrls.add(url);
+ instance.testUrls.add(url);
}
}
- var discoverer = getDiscoverer();
- Thread runner = instance.startDiscoverer(new PropertyChangeListener()
- {
-
- @Override
- public void propertyChange(PropertyChangeEvent evt)
++ var discoverer = getInstance();
+ discoverer.addServiceChangeListener((_discoverer, _services) -> {
+ if (discoverer.services != null)
{
- if (getInstance().services != null)
+ System.out.println("Changesupport: There are now "
+ + discoverer.services.size() + " services");
+ int i = 1;
- for (ServiceWithParameters instance : discoverer.services)
++ for (ServiceWithParameters s_instance : discoverer.services)
{
- System.out.println("Changesupport: There are now "
- + getInstance().services.size() + " services");
- int i = 1;
- for (Jws2Instance instance : getInstance().services)
- {
- System.out.println("Service " + i++ + " " + instance.getClass()
- + "@" + instance.getHost() + ": "
- + instance.getActionText());
- }
-
+ System.out.println(
- "Service " + i++ + " " + instance.getClass()
- + "@" + instance.getHostURL() + ": "
- + instance.getActionText());
++ "Service " + i++ + " " + s_instance.getClass()
++ + "@" + s_instance.getHostURL() + ": "
++ + s_instance.getActionText());
}
+
}
});
- while (runner.isAlive())
+ try
+ {
+ discoverer.startDiscoverer().get();
+ } catch (InterruptedException | ExecutionException e)
{
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException e)
- {
- }
}
try
{
}
}
- /**
- * Returns the singleton instance of this class.
- *
- * @return
- */
- public static Jws2Discoverer getDiscoverer()
- {
- if (discoverer == null)
- {
- discoverer = new Jws2Discoverer();
- }
- return discoverer;
- }
+
+ @Override
public boolean hasServices()
{
return !running && services != null && services.size() > 0;
}
+ @Override
public boolean isRunning()
{
return running;
}
+ @Override
public void setServiceUrls(List<String> wsUrls)
{
if (wsUrls != null && !wsUrls.isEmpty())
*
* @return
*/
+ @Override
public List<String> getServiceUrls()
{
if (testUrls != null)
return urls;
}
- public Vector<Jws2Instance> getServices()
+ @Override
+ public Vector<ServiceWithParameters> getServices()
{
- return (services == null) ? new Vector<>()
- : new Vector<>(services);
+ return (services == null) ? new Vector<>() : new Vector<>(services);
}
/**
* @param foo
* @return
*/
- public static boolean testServiceUrl(URL foo)
+ @Override
+ public boolean testServiceUrl(URL foo)
{
try
{
* @param changeSupport2
* @return new thread
*/
- public Thread startDiscoverer(PropertyChangeListener changeSupport2)
+ @Override
+ public CompletableFuture<WSDiscovererI> startDiscoverer()
{
/* if (restart())
{
{
setAborted(true);
}
- addPropertyChangeListener(changeSupport2);
- Thread thr = new Thread(this);
- thr.start();
- return thr;
+ CompletableFuture<WSDiscovererI> task = CompletableFuture
+ .supplyAsync(() -> {
+ run();
+ return Jws2Discoverer.this;
+ });
+ return task;
}
/**
* @return a human readable report of any problems with the service URLs used
* for discovery
*/
+ @Override
public String getErrorMessages()
{
if (!isRunning() && !isAborted())
return null;
}
+ @Override
public int getServerStatusFor(String url)
{
if (validServiceUrls != null && validServiceUrls.contains(url))
{
- return 1;
+ return STATUS_OK;
}
if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
{
- return 0;
+ return STATUS_NO_SERVICES;
}
if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
{
- return -1;
- }
- return -2;
- }
-
- /**
- * pick the user's preferred service based on a set of URLs (jaba server
- * locations) and service URIs (specifying version and service interface
- * class)
- *
- * @param serviceURL
- * @return null or best match for given uri/ls.
- */
- public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
- {
- HashSet<String> urls = new HashSet<>();
- urls.addAll(Arrays.asList(serviceURLs));
- Jws2Instance match = null;
- if (services != null)
- {
- for (Jws2Instance svc : services)
- {
- if (urls.contains(svc.getServiceTypeURI()))
- {
- if (match == null)
- {
- // for moment we always pick service from server ordered first in
- // user's preferences
- match = svc;
- }
- if (urls.contains(svc.getUri()))
- {
- // stop and return - we've matched type URI and URI for service
- // endpoint
- return svc;
- }
- }
- }
- }
- return match;
- }
-
- Map<String, Map<String, String>> preferredServiceMap = new HashMap<>();
-
- /**
- * get current preferred service of the given type, or global default
- *
- * @param af
- * null or a specific alignFrame
- * @param serviceType
- * Jws2Instance.serviceType for service
- * @return null if no service of this type is available, the preferred service
- * for the serviceType and af if specified and if defined.
- */
- public Jws2Instance getPreferredServiceFor(AlignFrame af,
- String serviceType)
- {
- String serviceurl = null;
- synchronized (preferredServiceMap)
- {
- String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
- Map<String, String> prefmap = preferredServiceMap.get(afid);
- if (afid.length() > 0 && prefmap == null)
- {
- // recover global setting, if any
- prefmap = preferredServiceMap.get("");
- }
- if (prefmap != null)
- {
- serviceurl = prefmap.get(serviceType);
- }
-
+ return STATUS_INVALID;
}
- Jws2Instance response = null;
- for (Jws2Instance svc : services)
- {
- if (svc.serviceType.equals(serviceType))
- {
- if (serviceurl == null || serviceurl.equals(svc.getHost()))
- {
- response = svc;
- break;
- }
- }
- }
- return response;
- }
-
- public void setPreferredServiceFor(AlignFrame af, String serviceType,
- String serviceAction, Jws2Instance selectedServer)
- {
- String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
- if (preferredServiceMap == null)
- {
- preferredServiceMap = new HashMap<>();
- }
- Map<String, String> prefmap = preferredServiceMap.get(afid);
- if (prefmap == null)
- {
- prefmap = new HashMap<>();
- preferredServiceMap.put(afid, prefmap);
- }
- prefmap.put(serviceType, selectedServer.getHost());
- prefmap.put(serviceAction, selectedServer.getHost());
- }
-
- public void setPreferredServiceFor(String serviceType,
- String serviceAction, Jws2Instance selectedServer)
- {
- setPreferredServiceFor(null, serviceType, serviceAction,
- selectedServer);
+ return STATUS_UNKNOWN;
}
/**
import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.api.JalviewServiceEndpointProviderI;
+import jalview.ws.api.MultipleSequenceAlignmentI;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.gui.MsaWSThread;
+import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.awt.event.ActionEvent;
import javax.swing.JMenuItem;
import javax.swing.ToolTipManager;
-import compbio.data.msa.MsaWS;
-import compbio.metadata.Argument;
-
/**
- * DOCUMENT ME!
+ * MsaWSClient
+ *
+ * Instantiates web service menu items for multiple alignment services, and
+ * holds logic for constructing a web service thread.
*
- * @author $author$
+ * TODO remove dependency on Jws2Client methods for creating AACon service UI
+ * elements.
+ *
+ * @author Jim Procter et al
* @version $Revision$
*/
-public class MsaWSClient extends Jws2Client
+public class MsaWSClient extends Jws2Client implements WSMenuEntryProviderI
{
/**
- * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+ * server is a proxy class implementing the core methods for submitting,
+ * monitoring and retrieving results from a multiple sequence alignment
+ * service
*/
- MsaWS server;
+ MultipleSequenceAlignmentI server;
- public MsaWSClient(Jws2Instance sh, String altitle,
+ public MsaWSClient(ServiceWithParameters sh, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
// TODO Auto-generated constructor stub
}
- public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
+ public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
+ String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
* DOCUMENT ME!
*/
- public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
- List<Argument> arguments, boolean editParams, String altitle,
+ public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
+ List<ArgumentI> arguments, boolean editParams, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
return;
}
- if (!(sh.service instanceof MsaWS))
+ if (!(sh instanceof JalviewServiceEndpointProviderI
+ && ((JalviewServiceEndpointProviderI) sh)
+ .getEndpoint() instanceof MultipleSequenceAlignmentI))
{
// redundant at mo - but may change
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.service_called_is_not_msa_service",
new String[]
- { sh.serviceType }),
+ { sh.getName() }),
MessageManager.getString("label.internal_jalview_error"),
JvOptionPane.WARNING_MESSAGE);
return;
}
- server = (MsaWS) sh.service;
+ serviceHandle = sh;
+ server = (MultipleSequenceAlignmentI) ((JalviewServiceEndpointProviderI) sh)
+ .getEndpoint();
if ((wsInfo = setWebService(sh, false)) == null)
{
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager
.formatMessage("label.msa_service_is_unknown", new String[]
- { sh.serviceType }),
+ { sh.getName() }),
MessageManager.getString("label.internal_jalview_error"),
JvOptionPane.WARNING_MESSAGE);
@Override
public void attachWSMenuEntry(JMenu rmsawsmenu,
- final Jws2Instance service, final AlignFrame alignFrame)
+ final ServiceWithParameters service, final AlignFrame alignFrame)
{
- if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+ if (Jws2ClientFactory.registerAAConWSInstance(rmsawsmenu,
+ service, alignFrame))
{
// Alignment dependent analysis calculation WS gui
return;
}
+ serviceHandle = service;
setWebService(service, true); // headless
+ attachWSMenuEntry(rmsawsmenu, alignFrame);
+ }
+
+ @Override
+ public void attachWSMenuEntry(JMenu wsmenu, AlignFrame alignFrame)
+ {
boolean finished = true, submitGaps = false;
- JMenu msawsmenu = rmsawsmenu;
+ /**
+ * temp variables holding msa service submenu or root service menu
+ */
+ JMenu msawsmenu = wsmenu;
+ JMenu rmsawsmenu = wsmenu;
String svcname = WebServiceName;
if (svcname.endsWith("WS"))
{
rmsawsmenu.add(msawsmenu);
calcName = "";
}
- boolean hasparams = service.hasParameters();
+ boolean hasparams = serviceHandle.hasParameters();
+ ServiceWithParameters service = (ServiceWithParameters) serviceHandle;
do
{
String action = "Align ";
--- /dev/null
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.jws2;
+
+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.SeqsetUtils;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureColourI;
+import jalview.api.PollableAlignCalcWorkerI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.IProgressIndicatorHandler;
+import jalview.gui.JvOptionPane;
+import jalview.gui.WebserviceInfo;
+import jalview.schemes.FeatureSettingsAdapter;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MapList;
+import jalview.util.MessageManager;
+import jalview.workers.AlignCalcWorker;
+import jalview.ws.JobStateSummary;
+import jalview.ws.api.CancellableI;
+import jalview.ws.api.JalviewServiceEndpointProviderI;
+import jalview.ws.api.JobId;
+import jalview.ws.api.SequenceAnnotationServiceI;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.api.WSAnnotationCalcManagerI;
+import jalview.ws.gui.AnnotationWsJob;
+import jalview.ws.jws2.dm.AAConSettings;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
+ implements WSAnnotationCalcManagerI, PollableAlignCalcWorkerI
+{
+
+ protected ServiceWithParameters service;
+
+ protected WsParamSetI preset;
+
+ protected List<ArgumentI> arguments;
+
+ protected IProgressIndicator guiProgress;
+
+ protected boolean submitGaps = true;
+
+ /**
+ * by default, we filter out non-standard residues before submission
+ */
+ protected boolean filterNonStandardResidues = true;
+
+ /**
+ * Recover any existing parameters for this service
+ */
+ protected void initViewportParams()
+ {
+ if (getCalcId() != null)
+ {
+ ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
+ getCalcId(),
+ new AAConSettings(true, service, this.preset, arguments),
+ true);
+ }
+ }
+
+ /**
+ *
+ * @return null or a string used to recover all annotation generated by this
+ * worker
+ */
+ public String getCalcId()
+ {
+ return service.getAlignAnalysisUI() == null ? null
+ : service.getAlignAnalysisUI().getCalcId();
+ }
+
+ public WsParamSetI getPreset()
+ {
+ return preset;
+ }
+
+ public List<ArgumentI> getArguments()
+ {
+ return arguments;
+ }
+
+ /**
+ * reconfigure and restart the AAConClient. This method will spawn a new
+ * thread that will wait until any current jobs are finished, modify the
+ * parameters and restart the conservation calculation with the new values.
+ *
+ * @param newpreset
+ * @param newarguments
+ */
+ public void updateParameters(final WsParamSetI newpreset,
+ final List<ArgumentI> newarguments)
+ {
+ preset = newpreset;
+ arguments = newarguments;
+ calcMan.startWorker(this);
+ initViewportParams();
+ }
+ protected boolean alignedSeqs = true;
+
+ protected boolean nucleotidesAllowed = false;
+
+ protected boolean proteinAllowed = false;
+
+ /**
+ * record sequences for mapping result back to afterwards
+ */
+ protected boolean bySequence = false;
+
+ protected Map<String, SequenceI> seqNames;
+
+ // TODO: convert to bitset
+ protected boolean[] gapMap;
+
+ int realw;
+
+ protected int start;
+
+ int end;
+
+ private AlignFrame alignFrame;
+
+ public boolean[] getGapMap()
+ {
+ return gapMap;
+ }
+
+ public SeqAnnotationServiceCalcWorker(ServiceWithParameters service,
+ AlignFrame alignFrame,
+ WsParamSetI preset, List<ArgumentI> paramset)
+ {
+ super(alignFrame.getCurrentView(), alignFrame.alignPanel);
+ // TODO: both these fields needed ?
+ this.alignFrame = alignFrame;
+ this.guiProgress = alignFrame;
+ this.preset = preset;
+ this.arguments = paramset;
+ this.service = service;
+ try
+ {
+ annotService = (jalview.ws.api.SequenceAnnotationServiceI) ((JalviewServiceEndpointProviderI) service)
+ .getEndpoint();
+ } catch (ClassCastException cce)
+ {
+ annotService = null;
- JvOptionPane.showMessageDialog(Desktop.desktop,
++ JvOptionPane.showMessageDialog(Desktop.getInstance(),
+ MessageManager.formatMessage(
+ "label.service_called_is_not_an_annotation_service",
+ new String[]
+ { service.getName() }),
+ MessageManager.getString("label.internal_jalview_error"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ }
+ cancellable = CancellableI.class.isInstance(annotService);
+ // configure submission flags
+ proteinAllowed = service.isProteinService();
+ nucleotidesAllowed = service.isNucleotideService();
+ alignedSeqs = service.isNeedsAlignedSequences();
+ bySequence = !service.isAlignmentAnalysis();
+ filterNonStandardResidues = service.isFilterSymbols();
+ min_valid_seqs = service.getMinimumInputSequences();
+ submitGaps = service.isAlignmentAnalysis();
+
+ if (service.isInteractiveUpdate())
+ {
+ initViewportParams();
+ }
+ }
+
+ /**
+ *
+ * @return true if the submission thread should attempt to submit data
+ */
+ public boolean hasService()
+ {
+ return annotService != null;
+ }
+
+ protected SequenceAnnotationServiceI annotService;
+ protected final boolean cancellable;
+
+ volatile JobId rslt = null;
+
+ AnnotationWsJob running = null;
+
+ private int min_valid_seqs;
+
+
+ private long progressId = -1;
+ JobStateSummary job = null;
+ WebserviceInfo info = null;
+ List<SequenceI> seqs = null;
+
+ @Override public void startUp() throws Throwable
+ {
+ if (alignViewport.isClosed())
+ {
+ abortAndDestroy();
+ return;
+ }
+ if (!hasService())
+ {
+ return;
+ }
+
+ StringBuffer msg = new StringBuffer();
+ job = new JobStateSummary();
+ info = new WebserviceInfo("foo", "bar", false);
+
+ seqs = getInputSequences(
+ alignViewport.getAlignment(),
+ bySequence ? alignViewport.getSelectionGroup() : null);
+
+ if (seqs == null || !checkValidInputSeqs(seqs))
+ {
+ jalview.bin.Cache.log.debug(
+ "Sequences for analysis service were null or not valid");
+ return;
+ }
+
+ if (guiProgress != null)
+ {
+ guiProgress.setProgressBar(service.getActionText(),
+ progressId = System.currentTimeMillis());
+ }
+ jalview.bin.Cache.log.debug("submitted " + seqs.size()
+ + " sequences to " + service.getActionText());
+
+ rslt = annotService.submitToService(seqs, getPreset(),
+ getArguments());
+ if (rslt == null)
+ {
+ return;
+ }
+ // TODO: handle job submission error reporting here.
+ Cache.log.debug("Service " + service.getUri() + "\nSubmitted job ID: "
+ + rslt);
+ ;
+ // ///
+ // otherwise, construct WsJob and any UI handlers
+ running = new AnnotationWsJob();
+ running.setJobHandle(rslt);
+ running.setSeqNames(seqNames);
+ running.setStartPos(start);
+ running.setSeqs(seqs);
+ job.updateJobPanelState(info, "", running);
+ if (guiProgress != null)
+ {
+ guiProgress.registerHandler(progressId,
+ new IProgressIndicatorHandler()
+ {
+
+ @Override
+ public boolean cancelActivity(long id)
+ {
+ calcMan.cancelWorker(SeqAnnotationServiceCalcWorker.this);
+ return true;
+ }
+
+ @Override
+ public boolean canCancel()
+ {
+ return cancellable;
+ }
+ });
+ }
+ }
+
+ @Override public boolean poll() throws Throwable
+ {
+ boolean finished = false;
+
+ Cache.log.debug("Updating status for annotation service.");
+ annotService.updateStatus(running);
+ job.updateJobPanelState(info, "", running);
+ if (running.isSubjobComplete())
+ {
+ Cache.log.debug(
+ "Finished polling analysis service job: status reported is "
+ + running.getState());
+ finished = true;
+ }
+ else
+ {
+ Cache.log.debug("Status now " + running.getState());
+ }
+
+ // pull any stats - some services need to flush log output before
+ // results are available
+ Cache.log.debug("Updating progress log for annotation service.");
+
+ try
+ {
+ annotService.updateJobProgress(running);
+ } catch (Throwable thr)
+ {
+ Cache.log.debug("Ignoring exception during progress update.",
+ thr);
+ }
+ Cache.log.trace("Result of poll: " + running.getStatus());
+
+
+ if (finished)
+ {
+ Cache.log.debug("Job poll loop exited. Job is " + running.getState());
+ if (running.isFinished())
+ {
+ // expect there to be results to collect
+ // configure job with the associated view's feature renderer, if one
+ // exists.
+ // TODO: here one would also grab the 'master feature renderer' in order
+ // to enable/disable
+ // features automatically according to user preferences
+ running.setFeatureRenderer(
+ ((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer());
+ Cache.log.debug("retrieving job results.");
+ final Map<String, FeatureColourI> featureColours = new HashMap<>();
+ final Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
+ List<AlignmentAnnotation> returnedAnnot = annotService
+ .getAnnotationResult(running.getJobHandle(), seqs,
+ featureColours, featureFilters);
+
+ Cache.log.debug("Obtained " + (returnedAnnot == null ? "no rows"
+ : ("" + returnedAnnot.size())));
+ Cache.log.debug("There were " + featureColours.size()
+ + " feature colours and " + featureFilters.size()
+ + " filters defined.");
+
+ // TODO
+ // copy over each annotation row reurned and also defined on each
+ // sequence, excluding regions not annotated due to gapMap/column
+ // visibility
+
+ // update calcId if it is not already set on returned annotation
+ if (returnedAnnot != null)
+ {
+ for (AlignmentAnnotation aa : returnedAnnot)
+ {
+ // assume that any CalcIds already set
+ if (getCalcId() != null && aa.getCalcId() == null
+ || "".equals(aa.getCalcId()))
+ {
+ aa.setCalcId(getCalcId());
+ }
+ // autocalculated annotation are created by interactive alignment
+ // analysis services
+ aa.autoCalculated = service.isAlignmentAnalysis()
+ && service.isInteractiveUpdate();
+ }
+ }
+
+ running.setAnnotation(returnedAnnot);
+
+ if (running.hasResults())
+ {
+ jalview.bin.Cache.log.debug("Updating result annotation from Job "
+ + rslt + " at " + service.getUri());
+ updateResultAnnotation(true);
+ if (running.isTransferSequenceFeatures())
+ {
+ // TODO
+ // look at each sequence and lift over any features, excluding
+ // regions
+ // not annotated due to gapMap/column visibility
+
+ jalview.bin.Cache.log.debug(
+ "Updating feature display settings and transferring features from Job "
+ + rslt + " at " + service.getUri());
+ // TODO: consider merge rather than apply here
+ alignViewport.applyFeaturesStyle(new FeatureSettingsAdapter()
+ {
+ @Override
+ public FeatureColourI getFeatureColour(String type)
+ {
+ return featureColours.get(type);
+ }
+
+ @Override
+ public FeatureMatcherSetI getFeatureFilters(String type)
+ {
+ return featureFilters.get(type);
+ }
+
+ @Override
+ public boolean isFeatureDisplayed(String type)
+ {
+ return featureColours.containsKey(type);
+ }
+
+ });
+ // TODO: JAL-1150 - create sequence feature settings API for
+ // defining
+ // styles and enabling/disabling feature overlay on alignment panel
+
+ if (alignFrame.alignPanel == ap)
+ {
+ alignViewport.setShowSequenceFeatures(true);
+ alignFrame.setMenusForViewport();
+ }
+ }
+ ap.adjustAnnotationHeight();
+ }
+ }
+ Cache.log.debug("Annotation Service Worker thread finished.");
+
+ }
+
+ return finished;
+ }
+
+ @Override public void cancel()
+ {
+ cancelCurrentJob();
+ }
+
+ @Override public void done()
+ {
+ if (ap != null)
+ {
+ if (guiProgress != null && progressId != -1)
+ {
+ guiProgress.removeProgressBar(progressId);
+ }
+ // TODO: may not need to paintAlignment again !
+ ap.paintAlignment(false, false);
+ }
+ }
+
+ /**
+ * validate input for dynamic/non-dynamic update context TODO: move to
+ * analysis interface ?
+ * @param seqs
+ *
+ * @return true if input is valid
+ */
+ boolean checkValidInputSeqs(List<SequenceI> seqs)
+ {
+ int nvalid = 0;
+ for (SequenceI sq : seqs)
+ {
+ if (sq.getStart() <= sq.getEnd()
+ && (sq.isProtein() ? proteinAllowed : nucleotidesAllowed))
+ {
+ if (submitGaps
+ || sq.getLength() == (sq.getEnd() - sq.getStart() + 1))
+ {
+ nvalid++;
+ }
+ }
+ }
+ return nvalid >= min_valid_seqs;
+ }
+
+ public void cancelCurrentJob()
+ {
+ try
+ {
+ String id = running.getJobId();
+ if (cancellable && ((CancellableI) annotService).cancel(running))
+ {
+ System.err.println("Cancelled job " + id);
+ }
+ else
+ {
+ System.err.println("Job " + id + " couldn't be cancelled.");
+ }
+ } catch (Exception q)
+ {
+ q.printStackTrace();
+ }
+ }
+
+ /**
+ * Interactive updating. Analysis calculations that work on the currently
+ * displayed alignment data should cancel existing jobs when the input data
+ * has changed.
+ *
+ * @return true if a running job should be cancelled because new input data is
+ * available for analysis
+ */
+ boolean isInteractiveUpdate()
+ {
+ return service.isInteractiveUpdate();
+ }
+
+ /**
+ * decide what sequences will be analysed TODO: refactor to generate
+ * List<SequenceI> for submission to service interface
+ *
+ * @param alignment
+ * @param inputSeqs
+ * @return
+ */
+ public List<SequenceI> getInputSequences(AlignmentI alignment,
+ AnnotatedCollectionI inputSeqs)
+ {
+ if (alignment == null || alignment.getWidth() <= 0
+ || alignment.getSequences() == null || alignment.isNucleotide()
+ ? !nucleotidesAllowed
+ : !proteinAllowed)
+ {
+ return null;
+ }
+ if (inputSeqs == null || inputSeqs.getWidth() <= 0
+ || inputSeqs.getSequences() == null
+ || inputSeqs.getSequences().size() < 1)
+ {
+ inputSeqs = alignment;
+ }
+
+ List<SequenceI> seqs = new ArrayList<>();
+
+ int minlen = 10;
+ int ln = -1;
+ if (bySequence)
+ {
+ seqNames = new HashMap<>();
+ }
+ gapMap = new boolean[0];
+ start = inputSeqs.getStartRes();
+ end = inputSeqs.getEndRes();
+ // TODO: URGENT! unify with JPred / MSA code to handle hidden regions
+ // correctly
+ // TODO: push attributes into WsJob instance (so they can be safely
+ // persisted/restored
+ for (SequenceI sq : (inputSeqs.getSequences()))
+ {
+ if (bySequence
+ ? sq.findPosition(end + 1)
+ - sq.findPosition(start + 1) > minlen - 1
+ : sq.getEnd() - sq.getStart() > minlen - 1)
+ {
+ String newname = SeqsetUtils.unique_name(seqs.size() + 1);
+ // make new input sequence with or without gaps
+ if (seqNames != null)
+ {
+ seqNames.put(newname, sq);
+ }
+ SequenceI seq;
+ if (submitGaps)
+ {
+ seqs.add(seq = new jalview.datamodel.Sequence(newname,
+ sq.getSequenceAsString()));
+ if (gapMap == null || gapMap.length < seq.getLength())
+ {
+ boolean[] tg = gapMap;
+ gapMap = new boolean[seq.getLength()];
+ System.arraycopy(tg, 0, gapMap, 0, tg.length);
+ for (int p = tg.length; p < gapMap.length; p++)
+ {
+ gapMap[p] = false; // init as a gap
+ }
+ }
+ for (int apos : sq.gapMap())
+ {
+ char sqc = sq.getCharAt(apos);
+ if (!filterNonStandardResidues
+ || (sq.isProtein() ? ResidueProperties.aaIndex[sqc] < 20
+ : ResidueProperties.nucleotideIndex[sqc] < 5))
+ {
+ gapMap[apos] = true; // aligned and real amino acid residue
+ }
+ ;
+ }
+ }
+ else
+ {
+ // TODO: add ability to exclude hidden regions
+ seqs.add(seq = new jalview.datamodel.Sequence(newname,
+ AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ sq.getSequenceAsString(start, end + 1))));
+ // for annotation need to also record map to sequence start/end
+ // position in range
+ // then transfer back to original sequence on return.
+ }
+ if (seq.getLength() > ln)
+ {
+ ln = seq.getLength();
+ }
+ }
+ }
+ if (alignedSeqs && submitGaps)
+ {
+ realw = 0;
+ for (int i = 0; i < gapMap.length; i++)
+ {
+ if (gapMap[i])
+ {
+ realw++;
+ }
+ }
+ // try real hard to return something submittable
+ // TODO: some of AAcon measures need a minimum of two or three amino
+ // acids at each position, and AAcon doesn't gracefully degrade.
+ for (int p = 0; p < seqs.size(); p++)
+ {
+ SequenceI sq = seqs.get(p);
+ // strip gapped columns
+ char[] padded = new char[realw],
+ orig = sq.getSequence();
+ for (int i = 0, pp = 0; i < realw; pp++)
+ {
+ if (gapMap[pp])
+ {
+ if (orig.length > pp)
+ {
+ padded[i++] = orig[pp];
+ }
+ else
+ {
+ padded[i++] = '-';
+ }
+ }
+ }
+ seqs.set(p, new jalview.datamodel.Sequence(sq.getName(),
+ new String(padded)));
+ }
+ }
+ return seqs;
+ }
+
+ @Override
+ public void updateAnnotation()
+ {
+ updateResultAnnotation(false);
+ }
+
+ public void updateResultAnnotation(boolean immediate)
+ {
+ if ((immediate || !calcMan.isWorking(this)) && running != null
+ && running.hasResults())
+ {
+ List<AlignmentAnnotation> ourAnnot = running.getAnnotation(),
+ newAnnots = new ArrayList<>();
+ //
+ // update graphGroup for all annotation
+ //
+ /**
+ * find a graphGroup greater than any existing ones this could be a method
+ * provided by alignment Alignment.getNewGraphGroup() - returns next
+ * unused graph group
+ */
+ int graphGroup = 1;
+ if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
+ {
+ for (AlignmentAnnotation ala : alignViewport.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (ala.graphGroup > graphGroup)
+ {
+ graphGroup = ala.graphGroup;
+ }
+ }
+ }
+ /**
+ * update graphGroup in the annotation rows returned from service
+ */
+ // TODO: look at sequence annotation rows and update graph groups in the
+ // case of reference annotation.
+ for (AlignmentAnnotation ala : ourAnnot)
+ {
+ if (ala.graphGroup > 0)
+ {
+ ala.graphGroup += graphGroup;
+ }
+ SequenceI aseq = null;
+
+ /**
+ * transfer sequence refs and adjust gapmap
+ */
+ if (ala.sequenceRef != null)
+ {
+ SequenceI seq = running.getSeqNames()
+ .get(ala.sequenceRef.getName());
+ aseq = seq;
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ }
+ Annotation[] resAnnot = ala.annotations,
+ gappedAnnot = new Annotation[Math.max(
+ alignViewport.getAlignment().getWidth(),
+ gapMap.length)];
+ for (int p = 0, ap = start; ap < gappedAnnot.length; ap++)
+ {
+ if (gapMap != null && gapMap.length > ap && !gapMap[ap])
+ {
+ gappedAnnot[ap] = new Annotation("", "", ' ', Float.NaN);
+ }
+ else if (p < resAnnot.length)
+ {
+ gappedAnnot[ap] = resAnnot[p++];
+ }
+ }
+ ala.sequenceRef = aseq;
+ ala.annotations = gappedAnnot;
+ AlignmentAnnotation newAnnot = getAlignViewport().getAlignment()
+ .updateFromOrCopyAnnotation(ala);
+ if (aseq != null)
+ {
+
+ aseq.addAlignmentAnnotation(newAnnot);
+ newAnnot.adjustForAlignment();
+
+ AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(
+ newAnnot, newAnnot.label, newAnnot.getCalcId());
+ }
+ newAnnots.add(newAnnot);
+
+ }
+ for (SequenceI sq : running.getSeqs())
+ {
+ if (!sq.getFeatures().hasFeatures()
+ && (sq.getDBRefs() == null || sq.getDBRefs().size() == 0))
+ {
+ continue;
+ }
+ running.setTransferSequenceFeatures(true);
+ SequenceI seq = running.getSeqNames().get(sq.getName());
+ SequenceI dseq;
+ ContiguousI seqRange = seq.findPositions(start, end);
+
+ while ((dseq = seq).getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ List<ContiguousI> sourceRange = new ArrayList();
+ if (gapMap != null && gapMap.length >= end)
+ {
+ int lastcol = start, col = start;
+ do
+ {
+ if (col == end || !gapMap[col])
+ {
+ if (lastcol <= (col - 1))
+ {
+ seqRange = seq.findPositions(lastcol, col);
+ sourceRange.add(seqRange);
+ }
+ lastcol = col + 1;
+ }
+ } while (++col <= end);
+ }
+ else
+ {
+ sourceRange.add(seq.findPositions(start, end));
+ }
+ int i = 0;
+ int source_startend[] = new int[sourceRange.size() * 2];
+
+ for (ContiguousI range : sourceRange)
+ {
+ source_startend[i++] = range.getBegin();
+ source_startend[i++] = range.getEnd();
+ }
+ Mapping mp = new Mapping(
+ new MapList(source_startend, new int[]
+ { seq.getStart(), seq.getEnd() }, 1, 1));
+ dseq.transferAnnotation(sq, mp);
+
+ }
+ updateOurAnnots(newAnnots);
+ }
+ }
+
+ protected void updateOurAnnots(List<AlignmentAnnotation> ourAnnot)
+ {
+ List<AlignmentAnnotation> our = ourAnnots;
+ ourAnnots = ourAnnot;
+ AlignmentI alignment = alignViewport.getAlignment();
+ if (our != null)
+ {
+ if (our.size() > 0)
+ {
+ for (AlignmentAnnotation an : our)
+ {
+ if (!ourAnnots.contains(an))
+ {
+ // remove the old annotation
+ alignment.deleteAnnotation(an);
+ }
+ }
+ }
+ our.clear();
+ }
+
+ // validate rows and update Alignmment state
+ for (AlignmentAnnotation an : ourAnnots)
+ {
+ alignViewport.getAlignment().validateAnnotation(an);
+ }
+ // TODO: may need a menu refresh after this
+ // af.setMenusForViewport();
+ ap.adjustAnnotationHeight();
+
+ }
+
+ public SequenceAnnotationServiceI getService()
+ {
+ return annotService;
+ }
+
+}
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
-import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
// TODO Auto-generated constructor stub
}
- public SequenceAnnotationWSClient(final Jws2Instance sh,
+ public SequenceAnnotationWSClient(final ServiceWithParameters sh,
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
super(alignFrame, preset, null);
// dan think. Do I need to change this method to run RNAalifold through the
// GUI
- public void initSequenceAnnotationWSClient(final Jws2Instance sh,
+ public void initSequenceAnnotationWSClient(final ServiceWithParameters sh,
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
// dan changed! dan test. comment out if conditional
// columns
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
- .getCalcManager().getRegisteredWorkersOfClass(clientClass);
- AbstractJabaCalcWorker worker;
- if (clnts == null || clnts.size() == 0)
+ .getCalcManager()
+ .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
+
+ SeqAnnotationServiceCalcWorker worker = null;
+ if (clnts != null)
+ {
+ for (AlignCalcWorkerI _worker : clnts)
+ {
+ worker = (SeqAnnotationServiceCalcWorker) _worker;
+ if (worker.hasService()
+ && worker.getService().getClass().equals(clientClass))
+ {
+ break;
+ }
+ worker = null;
+ }
+ }
+ if (worker == null)
{
if (!processParams(sh, editParams))
{
}
try
{
- worker = (AbstractJabaCalcWorker) (clientClass
- .getConstructor(new Class[]
- { Jws2Instance.class, AlignFrame.class, WsParamSetI.class,
- List.class })
- .newInstance(new Object[]
- { sh, alignFrame, this.preset, paramset }));
+ worker = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset,
+ paramset);
} catch (Exception x)
{
x.printStackTrace();
MessageManager.getString("error.implementation_error"),
x);
}
- alignFrame.getViewport().getCalcManager().registerWorker(worker);
- alignFrame.getViewport().getCalcManager().startWorker(worker);
-
+ alignFrame.getViewport().getCalcManager().registerWorker(worker); // also
+ // starts
+ // the
+ // worker
}
else
{
- worker = (AbstractJabaCalcWorker) clnts.get(0);
if (editParams)
{
paramset = worker.getArguments();
worker.updateParameters(this.preset, paramset);
}
}
- if (sh.action.toLowerCase().contains("disorder"))
+ if (!sh.isInteractiveUpdate())
{
// build IUPred style client. take sequences, returns annotation per
// sequence.
}
alignFrame.getViewport().getCalcManager().startWorker(
- new AADisorderClient(sh, alignFrame, preset, paramset));
+ new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
}
}
- public SequenceAnnotationWSClient(AAConSettings fave,
+ public SequenceAnnotationWSClient(AutoCalcSetting fave,
AlignFrame alignFrame, boolean b)
{
- super(alignFrame, fave.getPreset(), fave.getJobArgset());
+ super(alignFrame, fave.getPreset(), fave.getArgumentSet());
initSequenceAnnotationWSClient(fave.getService(), alignFrame,
fave.getPreset(), b);
}
* @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
* jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
*/
- public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
+ @Override
+ public void attachWSMenuEntry(JMenu wsmenu,
+ final ServiceWithParameters service,
final AlignFrame alignFrame)
{
- if (registerAAConWSInstance(wsmenu, service, alignFrame))
+ if (Jws2ClientFactory.registerAAConWSInstance(wsmenu,
+ service, alignFrame))
{
// Alignment dependent analysis calculation WS gui
return;
}
boolean hasparams = service.hasParameters();
- // Assume name ends in WS
- String calcName = service.serviceType.substring(0,
- service.serviceType.length() - 2);
+ String calcName = service.getName();
+ if (calcName.endsWith("WS"))
+ {
+ // Remove "WS" suffix
+ calcName = calcName.substring(0, calcName.length() - 2);
+ }
JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
"label.calcname_with_default_settings", new String[]
@Override
public void actionPerformed(ActionEvent e)
{
- new SequenceAnnotationWSClient(service, alignFrame, null, false);
+ new SequenceAnnotationWSClient(service, alignFrame,
+ null, false);
}
});
wsmenu.add(annotservice);
annotservice.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- new SequenceAnnotationWSClient(service, alignFrame, null, true);
+ new SequenceAnnotationWSClient(service, alignFrame,
+ null, true);
}
});
wsmenu.add(annotservice);
+ "</strong><br/>" + preset.getDescription()));
methodR.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- new SequenceAnnotationWSClient(service, alignFrame, preset,
+ new SequenceAnnotationWSClient(service,
+ alignFrame, preset,
false);
}
{
annotservice = new JMenuItem(
MessageManager.getString("label.view_documentation"));
- if (service.docUrl != null)
+ if (service != null && service.hasDocumentationUrl())
{
annotservice.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent arg0)
{
- Desktop.instance.showUrl(service.getDocumentationUrl());
- Desktop.getInstance().showUrl(service.docUrl);
++ Desktop.getInstance().showUrl(service.getDocumentationUrl());
}
});
annotservice.setToolTipText(
JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
"label.view_service_doc_url", new String[]
- { service.docUrl, service.docUrl })));
+ { service.getDocumentationUrl(),
+ service.getDocumentationUrl() })));
wsmenu.add(annotservice);
}
}
*/
package jalview.ws.jws2.jabaws2;
-import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.util.MessageManager;
+import jalview.ws.api.JalviewServiceEndpointProviderI;
+import jalview.ws.api.ServiceWithParameters;
import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.MsaWSClient;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
import java.io.Closeable;
-
-import javax.swing.JMenu;
+import java.net.URL;
import compbio.data.msa.JABAService;
import compbio.data.msa.MsaWS;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
-public class Jws2Instance implements AutoCloseable
+public class Jws2Instance extends ServiceWithParameters
+ implements JalviewServiceEndpointProviderI, AutoCloseable
{
public JABAService service;
- public String description;
-
- public String docUrl;
-
/**
*
* @param hosturl
public Jws2Instance(String hosturl, String serviceType, String action,
String description, JABAService service)
{
- super();
- this.hosturl = hosturl;
- this.serviceType = serviceType;
+ super(action, action, serviceType, description, hosturl);
this.service = service;
- this.action = action;
- this.description = description;
+ if (service instanceof MsaWS<?>)
+ {
+ style = ServiceClient.MSAWSCLIENT;
+ }
+ else if (service instanceof SequenceAnnotation<?>)
+ {
+ style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
+ }
+
int p = description.indexOf("MORE INFORMATION:");
if (p > -1)
{
- docUrl = description.substring(description.indexOf("http", p)).trim();
+ String docUrl = description.substring(description.indexOf("http", p))
+ .trim();
if (docUrl.indexOf('\n') > -1)
{
docUrl = docUrl.substring(0, docUrl.indexOf("\n")).trim();
}
+ if (docUrl.length() > 0)
+ {
+ try
+ {
+ URL url = new URL(docUrl);
+ if (url != null)
+ {
+ setDocumentationUrl(docUrl);
+ }
+ } catch (Exception x)
+ {
+
+ }
+ }
}
}
} catch (Exception ex)
{
System.err.println("Exception when retrieving presets for service "
- + serviceType + " at " + hosturl);
+ + getServiceType() + " at " + getHostURL());
}
}
return presets;
}
- public String getHost()
- {
- return hosturl;
- /*
- * try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80) {
- * return serviceurl.getHost()+":"+serviceurl.getPort(); } return
- * serviceurl.getHost(); } catch (Exception e) {
- * System.err.println("Failed to parse service URL '" + hosturl +
- * "' as a valid URL!"); } return null;
- */
- }
-
- /**
- * @return short description of what the service will do
- */
- public String getActionText()
- {
- return action + " with " + serviceType;
- }
-
/**
* non-thread safe - blocks whilst accessing service to get complete set of
* available options and parameters
throw new Error(MessageManager.formatMessage(
"error.implementation_error_runner_config_not_available",
new String[]
- { serviceType, service.getClass().toString() }));
+ { getServiceType(), service.getClass().toString() }));
}
@Override
// super.finalize();
}
+ @Override
public ParamDatastoreI getParamStore()
{
if (paramStore == null)
try
{
paramStore = new JabaParamStore(this,
- (Desktop.instance != null ? Desktop.getUserParameterStore()
+ (Desktop.getInstance() != null ? Desktop.getUserParameterStore()
: null));
} catch (Exception ex)
{
return paramStore;
}
- public String getUri()
- {
- // this is only valid for Jaba 1.0 - this formula might have to change!
- return hosturl
- + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? ""
- : "/")
- + serviceType;
- }
-
private boolean hasParams = false, lookedForParams = false;
+ @Override
public boolean hasParameters()
{
if (!lookedForParams)
return hasParams;
}
- public void attachWSMenuEntry(JMenu atpoint, AlignFrame alignFrame)
+ /**
+ * initialise a parameter store for this service
+ *
+ * @param userParameterStore
+ * - the user ParamManager (e.g. Desktop.getUserParameterStore() )
+ */
+ @Override
+ public void initParamStore(ParamManager userParameterStore)
{
- if (service instanceof MsaWS<?>)
- {
- new MsaWSClient().attachWSMenuEntry(atpoint, this, alignFrame);
- }
- else if (service instanceof SequenceAnnotation<?>)
+ if (paramStore == null)
{
- new SequenceAnnotationWSClient().attachWSMenuEntry(atpoint, this,
- alignFrame);
+ paramStore = new JabaParamStore(this, userParameterStore);
}
}
- public String getServiceTypeURI()
+ /**
+ * an object that implements one or more interfaces in jalview.ws.api
+ *
+ * @return
+ */
+ @Override
+ public Object getEndpoint()
{
- return "java:" + serviceType;
- }
-
- jalview.ws.uimodel.AlignAnalysisUIText aaui;
+ if (service instanceof MsaWS<?>)
+ {
+ if (aaui != null)
+ {
+ throw new Error(
+ "JABAWS MsaWS based instant calculation not implemented.");
- public jalview.ws.uimodel.AlignAnalysisUIText getAlignAnalysisUI()
- {
- return aaui;
+ }
+ else
+ {
+ return new JabawsMsaInstance(this);
+ }
+ }
+ else
+ {
+ if (service instanceof compbio.data.msa.SequenceAnnotation)
+ {
+ if (aaui != null)
+ {
+ try
+ {
+ // probably a factory would be nicer but..
+ return aaui.getClient().getConstructor(getClass())
+ .newInstance(this);
+ } catch (Throwable t)
+ {
+ throw new Error("Implementation Error in web service framework",
+ t);
+ }
+ }
+ return new AADisorderClient(this);
+ }
+ return null;
+ }
}
}
*/
package jalview.ws.jws2.jabaws2;
+ import jalview.bin.ApplicationSingletonProvider;
+ import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
-import jalview.ws.jws2.AAConClient;
-import jalview.ws.jws2.RNAalifoldClient;
++
import jalview.ws.uimodel.AlignAnalysisUIText;
import java.util.HashMap;
import compbio.data.msa.JABAService;
- public class Jws2InstanceFactory
+ public class Jws2InstanceFactory implements ApplicationSingletonI
{
- private static HashMap<String, AlignAnalysisUIText> aaConGUI;
- private static HashSet<String> ignoreGUI;
+ private Jws2InstanceFactory()
+ {
+ // private singleton
+ }
+
+ private static Jws2InstanceFactory getInstance()
+ {
+ return (Jws2InstanceFactory) ApplicationSingletonProvider
+ .getInstance(Jws2InstanceFactory.class);
+ }
+
+ private HashMap<String, AlignAnalysisUIText> aaConGUI;
+
+ private HashSet<String> ignoreGUI;
private static String category_rewrite(String cat_name)
{
: cat_name;
}
- private static void init()
+ private void init()
{
if (aaConGUI == null)
{
aaConGUI = new HashMap<>();
aaConGUI.put(compbio.ws.client.Services.AAConWS.toString(),
- AAConClient.getAlignAnalysisUITest());
+ AAConClient.getAlignAnalysisUIText());
aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
- RNAalifoldClient.getAlignAnalysisUITest());
+ RNAalifoldClient.getAlignAnalysisUIText());
// ignore list for JABAWS services not supported in jalview ...
ignoreGUI = new HashSet<>();
}
*/
public static boolean ignoreService(String serviceType)
{
- init();
- return (ignoreGUI.contains(serviceType.toString()));
+ getInstance().init();
+ return (getInstance().ignoreGUI.contains(serviceType.toString()));
}
/**
String serviceType, String name, String description,
JABAService service)
{
- init();
+ getInstance().init();
Jws2Instance svc = new Jws2Instance(jwsservers, serviceType,
category_rewrite(name), description, service);
- svc.setAlignAnalysisUI(aaConGUI.get(serviceType.toString()));
- svc.aaui = getInstance().aaConGUI.get(serviceType.toString());
++ svc.setAlignAnalysisUI(getInstance().aaConGUI.get(serviceType.toString()));
return svc;
}
*/
package jalview.ws.rest;
+ import jalview.bin.ApplicationSingletonProvider;
+ import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
-import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.MessageManager;
import jalview.ws.WSClient;
import jalview.ws.WSClientI;
import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.rest.clientdefs.ShmrRestClient;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.Hashtable;
import java.util.Vector;
import javax.swing.JMenu;
*
*/
public class RestClient extends WSClient
- implements WSClientI, WSMenuEntryProviderI
+ implements WSClientI, WSMenuEntryProviderI, ApplicationSingletonI
{
+
+ @SuppressWarnings("unused")
+ private RestClient()
+ {
+ // accessed by ApplicationSingletonProvider
+ }
+
+
+ private static RestClient getInstance()
+ {
+ return (RestClient) ApplicationSingletonProvider.getInstance(RestClient.class);
+ }
+
+ public static final String RSBS_SERVICES = "RSBS_SERVICES";
+
+
+ protected Vector<String> services = null;
+
+
RestServiceDescription service;
public RestClient(RestServiceDescription rsd)
{
WebServiceJobTitle = MessageManager
.formatMessage("label.webservice_job_title", new String[]
- { service.details.Action, service.details.Name });
- WebServiceName = service.details.Name;
+ { service.details.getAction(), service.details.getName() });
+ WebServiceName = service.details.getName();
WebServiceReference = "No reference - go to url for more info";
- if (service.details.description != null)
+ if (service.details.getDescription() != null)
{
- WebServiceReference = service.details.description;
+ WebServiceReference = service.details.getDescription();
}
if (!headless)
{
wsInfo = new WebserviceInfo(WebServiceJobTitle,
- WebServiceName + "\n" + WebServiceReference, true);
+ WebServiceName + "\n" + WebServiceReference, Desktop.FRAME_MAKE_VISIBLE);
wsInfo.setRenderAsHtml(true);
}
public void attachWSMenuEntry(final JMenu wsmenu,
final AlignFrame alignFrame)
{
- JMenuItem submit = new JMenuItem(service.details.Name);
+ JMenuItem submit = new JMenuItem(service.details.getName());
submit.setToolTipText(MessageManager
.formatMessage("label.rest_client_submit", new String[]
- { service.details.Action, service.details.Name }));
+ { service.details.getAction(), service.details.getName() }));
submit.addActionListener(new ActionListener()
{
else
{
// TODO: try to tell the user why the job couldn't be started.
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
(jobsthread.hasWarnings() ? jobsthread.getWarnings()
: MessageManager.getString(
"label.job_couldnt_be_started_check_input")),
}
}
- public static RestClient makeShmmrRestClient()
- {
- String action = "Analysis",
- description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)",
- name = MessageManager.getString("label.multiharmony");
- Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
- jalview.ws.rest.params.JobConstant toolp;
- // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
- // iparams.put(toolp.token, toolp);
- // toolp = new
- // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("blast","0");
- // iparams.put(toolp.token, toolp);
-
- jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
- // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
- // so we always upload our files.
- aliinput.token = "ali_file";
- aliinput.writeAsFile = true;
- iparams.put(aliinput.token, aliinput);
- jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
- sgroups.setMinsize(2);
- sgroups.min = 2;// need at least two group defined to make a partition
- iparams.put("groups", sgroups);
- sgroups.token = "groups";
- sgroups.sep = " ";
- RestServiceDescription shmrService = new RestServiceDescription(action,
- description, name,
- "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview", // ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
- "?tool=jalview", iparams, true, false, '-');
- // a priori knowledge of the data returned from the service
- shmrService.addResultDatatype(JvDataType.ANNOTATION);
- return new RestClient(shmrService);
- }
-
public AlignmentPanel recoverAlignPanelForView()
{
AlignmentPanel[] aps = Desktop
return true;
}
- protected static Vector<String> services = null;
-
- public static final String RSBS_SERVICES = "RSBS_SERVICES";
-
public static RestClient[] getRestClients()
{
+ return getInstance().getClients();
+ }
+
+ private RestClient[] getClients()
+ {
if (services == null)
{
- services = new Vector<String>();
+ services = new Vector<>();
try
{
for (RestServiceDescription descr : RestServiceDescription
- .parseDescriptions(
- jalview.bin.Cache.getDefault(RSBS_SERVICES,
- makeShmmrRestClient().service.toString())))
+ .parseDescriptions(jalview.bin.Cache.getDefault(
+ RSBS_SERVICES,
+ ShmrRestClient.makeShmmrRestClient().service.toString())))
{
services.add(descr.toString());
}
public String getAction()
{
- return service.details.Action;
+ return service.details.getAction();
}
public RestServiceDescription getRestDescription()
public static Vector<String> getRsbsDescriptions()
{
- Vector<String> rsbsDescrs = new Vector<String>();
+ Vector<String> rsbsDescrs = new Vector<>();
for (RestClient rsbs : getRestClients())
{
rsbsDescrs.add(rsbs.getRestDescription().toString());
{
if (rsbsUrls != null)
{
+
// TODO: consider validating services ?
- services = new Vector<>(rsbsUrls);
+ getInstance().services = new Vector<String>(rsbsUrls);
StringBuffer sprop = new StringBuffer();
- for (String s : services)
+ for (String s : getInstance().services)
{
sprop.append(s);
}
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
- import jalview.analysis.AlignmentGenerator;
- import jalview.commands.EditCommand;
- import jalview.commands.EditCommand.Action;
- import jalview.datamodel.PDBEntry.Type;
- import jalview.gui.JvOptionPane;
- import jalview.util.MapList;
-
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+ import jalview.analysis.AlignmentGenerator;
+ import jalview.commands.EditCommand;
+ import jalview.commands.EditCommand.Action;
+ import jalview.datamodel.PDBEntry.Type;
+ import jalview.gui.JvOptionPane;
+ import jalview.util.MapList;
++
import junit.extensions.PA;
public class SequenceTest
* invalid inputs
*/
assertNull(sq.findPositions(6, 5));
- assertNull(sq.findPositions(0, 5));
- assertNull(sq.findPositions(-1, 5));
/*
* all gapped ranges
assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE
assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
assertEquals(new Range(8, 13), sq.findPositions(1, 99));
+
+ /**
+ * now try on a sequence with no gaps
+ */
+ sq.createDatasetSequence();
+ assertEquals(new Range(8, 13),
+ sq.getDatasetSequence().findPositions(1, 99));
+ assertEquals(new Range(8, 13),
+ sq.getDatasetSequence().findPositions(0, 99));
+
}
/**
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
public class AlignFrameTest
{
@AfterMethod(alwaysRun = true)
public void tearDown()
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
}
/**
public void setUp()
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Cache.setPropertyNoSave("SHOW_IDENTITY",
Boolean.TRUE.toString());
af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
DataSourceType.FILE);
@Test(groups = "Functional")
public void testChangeColour_background_groupsAndThresholds()
{
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
AlignmentI al = av.getAlignment();
/*
@Test(groups = "Functional")
public void testColourThresholdActions()
{
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
AlignmentI al = av.getAlignment();
/*
@Test(groups = "Functional")
public void testNewView_colourThresholds()
{
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
AlignmentI al = av.getAlignment();
/*
*/
af.newView_actionPerformed(null);
assertEquals(af.alignPanel.getViewName(), "View 1");
- AlignViewport av2 = af.getViewport();
+ AlignmentViewport av2 = af.getViewport();
assertNotSame(av, av2);
assertSame(av2, af.alignPanel.av);
rs = av2.getResidueShading();
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.api.AlignViewportI;
import java.util.ArrayList;
import java.util.List;
import jalview.schemes.PIDColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.util.MapList;
+import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
+ import jalview.workers.AlignCalcManager;
public class AlignViewportTest
{
AlignmentI al;
- AlignViewport testee;
+ AlignmentViewport testee;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- Jalview.main(new String[] { "-nonews", "-props",
+ Jalview.main(new String[] {
+ //"-jabaws", "none",
+ "-nonews", "-props",
"test/jalview/testProps.jvprops" });
/*
* remove any sequence mappings left lying around by other tests
*/
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.resetAll();
}
* mappings
*/
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
assertEquals(2, sequenceMappings.size());
assertTrue(sequenceMappings.contains(acf1));
@Test(groups = { "Functional" })
public void testDeregisterMapping_withNoReference()
{
- Desktop d = Desktop.instance;
+ Desktop d = Desktop.getInstance();
assertNotNull(d);
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.resetAll();
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
@Test(groups = { "Functional" })
public void testDeregisterMapping_withReference()
{
- Desktop d = Desktop.instance;
+ Desktop d = Desktop.getInstance();
assertNotNull(d);
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.resetAll();
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
@Test(groups = { "Functional" }, timeOut=2000)
public void testUpdateConservation_qualityOnly()
{
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Cache.setPropertyNoSave("SHOW_QUALITY",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave("SHOW_CONSERVATION",
Boolean.FALSE.toString());
- Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
+ Cache.setPropertyNoSave("SHOW_OCCUPANCY",
Boolean.FALSE.toString());
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Cache.setPropertyNoSave("SHOW_IDENTITY",
Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
{
synchronized (this)
{
- while (viewport.getCalcManager().isWorking())
+ System.out.print("waiting...");
+ int n = 3;
+ while (--n >= 0 || viewport.getCalcManager().isWorking())
{
try
{
+ System.out.print(((AlignCalcManager) viewport.getCalcManager()).getQueueLength());
wait(50);
} catch (InterruptedException e)
{
}
}
+ System.out.println("...done");
}
}
/*
* test for JAL-2283: don't inadvertently turn on colour by conservation
*/
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave("DEFAULT_COLOUR_PROT", "None");
+ Cache.setPropertyNoSave("SHOW_CONSERVATION",
Boolean.TRUE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
SequenceGroup sg1 = new SequenceGroup();
SequenceGroup sg2 = new SequenceGroup();
SequenceGroup sg3 = new SequenceGroup();
jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport av = af.getViewport();
- Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row.");
+ AlignViewportI av = af.getViewport();
+ Assert.assertNull(av.getAlignmentGapAnnotation(),
+ "Preference did not disable occupancy row.");
int c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
null, "Occupancy"))
af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
av = af.getViewport();
- Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
+ Assert.assertNotNull(av.getAlignmentGapAnnotation(),
+ "Preference did not enable occupancy row.");
c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
null, av.getAlignmentGapAnnotation().label))
AlignViewport testme = af.getViewport();
waitForCalculations(testme);
SequenceI cons = testme.getConsensusSeq();
- assertEquals("A-C", cons.getSequenceAsString());
+ String s = cons.getSequenceAsString();
+ System.out.println("s is " + s);
+
+ assertEquals("A-C", s);
}
@Test(groups = { "Functional" })
import static org.testng.Assert.assertEquals;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-
import javax.swing.JTextArea;
-import junit.extensions.PA;
-
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class PairwiseAlignmentPanelTest
{
@Test(groups = "Functional")
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
AlignmentI al = viewport.getAlignment();
/*
PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
- String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
+ String text = ((JTextArea) PA.getValue(testee, "textarea")).getText().replace("\r\n", "\n");
String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
+ "Sequence FER1_PEA/29-32 (Sequence length = 7)\n"
+ "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
String seqs = ">Q93XJ9_SOLTU/23-29\nL-KAISNV\n>FER1_PEA/26-32\nV-TTTKAF\n";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
DataSourceType.PASTE);
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
- String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
+ String text = ((JTextArea) PA.getValue(testee, "textarea")).getText().replace("\r\n", "\n");
String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
+ "Sequence FER1_PEA/29-32 (Sequence length = 7)\n"
+ "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertTrue(menu.isEnabled());
String s = MessageManager.getString("label.add_annotations_for");
- String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
- + "<div class=\"ttip\">" + s
- + "<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
+ // String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
+ // + "<div class=\"ttip\">" + s
+ // + "<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
+ String expected = "<html>" + s + "<br>Jmol/secondary structure<br>PDB/Temp</html>";
assertEquals(expected, menu.getToolTipText());
}
testee.configureReferenceAnnotationsMenu(menu, seqs);
assertTrue(menu.isEnabled());
String s = MessageManager.getString("label.add_annotations_for");
- String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
- + "<div class=\"ttip\">" + s
- + "<br/>Jmol/secondary structure<br/>PDB/Temp </div></html>";
- assertEquals(expected, menu.getToolTipText());
+ // String expected = "<html><style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style>"
+ // + "<div class=\"ttip\">" + s
+ // + "<br/>Jmol/secondary structure<br/>PDB/Temp</html>";
+ String expected = "<html>" + s
+ + "<br>Jmol/secondary structure<br>PDB/Temp</html>";
+ s = menu.getToolTipText();
+ assertEquals(expected, s);
}
/**
// PDB.secondary structure on Sequence0
AlignmentAnnotation annotation = new AlignmentAnnotation(
"secondary structure", "", 0);
+ annotation.annotations = new Annotation[] { new Annotation(2f) };
annotation.setCalcId("PDB");
seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
if (addToSequence)
// PDB.Temp on Sequence1
annotation = new AlignmentAnnotation("Temp", "", 0);
annotation.setCalcId("PDB");
+ annotation.annotations = new Annotation[] { new Annotation(2f) };
seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
if (addToSequence)
{
// JMOL.secondary structure on Sequence0
annotation = new AlignmentAnnotation("secondary structure", "", 0);
annotation.setCalcId("Jmol");
+ annotation.annotations = new Annotation[] { new Annotation(2f) };
seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
if (addToSequence)
{
--- /dev/null
+package jalview.hmmer;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.io.HMMFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.simple.Option;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class HMMERTest {
+
+ AlignFrame frame;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpBeforeClass() throws Exception
+ {
+ /*
+ * NB: check HMMER_PATH in testProps.jvprops is valid for
+ * the machine on which this runs
+ */
+ Jalview.main(
+ new String[]
+ { "-noquestionnaire", "-nonews", "-props",
+ "test/jalview/hmmer/testProps.jvprops", "-open",
+ "examples/uniref50.fa" });
+ frame = Desktop.getAlignFrames()[0];
+ }
+
+ @AfterClass(alwaysRun = true)
+ public static void tearDownAfterClass() throws Exception
+ {
- Desktop.instance.closeAll_actionPerformed(null);
++ Desktop.getInstance().closeAll_actionPerformed(null);
+ }
+
+ /**
+ * Test with a dependency on locally installed hmmbuild binaries
+ *
+ * @throws MalformedURLException
+ * @throws IOException
+ */
+ @Test(groups = "External")
+ public void testHMMBuildThenHMMAlign()
+ throws MalformedURLException, IOException
+ {
+ /*
+ * run hmmbuild
+ */
+ testHMMBuild();
+ List<SequenceI> hmms = frame.getViewport().getAlignment()
+ .getHmmSequences();
+ assertFalse(hmms.isEmpty());
+
+ /*
+ * now run hmmalign - by default with respect to the added HMM profile
+ */
+ testHMMAlign();
+ }
+
+ public void testHMMBuild()
+ {
+ /*
+ * set up argument to run hmmbuild for the alignment
+ */
+ ArrayList<ArgumentI> params = new ArrayList<>();
+ String argName = MessageManager.getString("label.hmmbuild_for");
+ String argValue = MessageManager.getString("label.alignment");
+ params.add(
+ new Option(argName, null, false, null, argValue, null, null));
+
+ HMMBuild builder = new HMMBuild(frame, params);
+ builder.run();
+
+ SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
+ HiddenMarkovModel hmm = seq.getHMM();
+ assertNotNull(hmm);
+
+ assertEquals(hmm.getLength(), 148);
+ assertEquals(hmm.getAlphabetType(), "amino");
+ assertEquals(hmm.getName(), "Alignment_HMM");
+ assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
+ "0.648193");
+ }
+
+ public void testHMMAlign()
+ {
+ HmmerCommand thread = new HMMAlign(frame,
+ new ArrayList<ArgumentI>());
+ thread.run();
+
+ AlignFrame[] alignFrames = Desktop.getAlignFrames();
+ if (alignFrames == null)
+ {
+ fail("No align frame loaded");
+ }
+
+ /*
+ * now have the original align frame, and another for realigned sequences
+ */
+ assertEquals(alignFrames.length, 2);
+ AlignmentI original = alignFrames[0].getViewport().getAlignment();
+ assertNotNull(original);
+ AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
+ assertNotNull(realigned);
+ assertFalse(original.getHmmSequences().isEmpty());
+ assertFalse(realigned.getHmmSequences().isEmpty());
+
+ SequenceI ferCapan = original.findName("FER_CAPAN");
+ assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
+
+ SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
+ assertTrue(ferCapanRealigned.getSequenceAsString()
+ .startsWith("-------m-A----SVSAT"));
+ }
+}
+
@Test(groups = "Functional")
public void testGetReadableFormats()
{
- String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
- String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, BSML]";
++ String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getReadableFormats().toString(), expected);
}
@Test(groups = "Functional")
public void testGetWritableFormats()
{
- String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
+ String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getWritableFormats(true).toString(), expected);
- expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview]";
+ expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview, HMMER3]";
assertEquals(formats.getWritableFormats(false).toString(), expected);
}
@Test(groups = "Functional")
public void testDeregisterFileFormat()
{
- String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
- String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, BSML]";
+ String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
- String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
++ String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML]";
FileFormats formats = FileFormats.getInstance();
+ System.out.println(formats.getReadableFormats().toString());
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
formats.deregisterFileFormat(FileFormat.Fasta.getName());
- writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, BSML]";
+ writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
++ readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML]";
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
* re-register the format: it gets added to the end of the list
*/
formats.registerFileFormat(FileFormat.Fasta);
- writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, BSML, Fasta]";
+ writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3, Fasta]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, Fasta]";
++ readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, BSML, Fasta]";
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
}
import org.testng.Assert;
import org.testng.AssertJUnit;
+ import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLocus;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import junit.extensions.PA;
+
@Test(singleThreaded = true)
public class Jalview2xmlTests extends Jalview2xmlBase
{
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ Desktop.getInstance().closeAll_actionPerformed(null);
+ }
@Override
@BeforeClass(alwaysRun = true)
DataSourceType.FILE);
assertNotNull(af, "Didn't read input file " + inFile);
af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
assertSame(viewport.getGlobalColourScheme().getClass(),
TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
assertNotNull(
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
- assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
+ assertEquals(Desktop.getAlignFrames().length,
+ 1 + origCount,
"Didn't gather the views in the example file.");
-
}
/**
@Test(groups = { "Functional" }, enabled = true)
public void testStoreAndRecoverExpandedviews() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
{
Assert.fail("Didn't save the expanded view state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@Test(groups = { "Functional" })
public void testStoreAndRecoverReferenceSeqSettings() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
{
Assert.fail("Didn't save the expanded view state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@Test(groups = { "Functional" })
public void testStoreAndRecoverGroupRepSeqs() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
{
Assert.fail("Didn't save the expanded view state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@Test(groups = { "Functional" })
public void testStoreAndRecoverPDBEntry() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
String exampleFile = "examples/3W5V.pdb";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
DataSourceType.FILE);
{
Assert.fail("Didn't save the state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@Test(groups = { "Functional" })
public void testStoreAndRecoverColourThresholds() throws IOException
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
AlignmentI al = av.getAlignment();
/*
".jvp");
tfile.deleteOnExit();
new Jalview2XML(false).saveState(tfile);
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
DataSourceType.FILE);
Assert.assertNotNull(af, "Failed to reload project");
}
/**
+ * Load an HMM profile to an alignment, and confirm it is correctly restored
+ * when reloaded from project
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverHmmProfile() throws IOException
+ {
- Desktop.instance.closeAll_actionPerformed(null);
++ Desktop.getInstance().closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+
+ AlignViewportI av = af.getViewport();
+ AlignmentI al = av.getAlignment();
+
+ /*
+ * mimic drag and drop of hmm file on to alignment
+ */
+ AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.hmm", DataSourceType.FILE);
+ al.insertSequenceAt(0,
+ af2.getViewport().getAlignment().getSequenceAt(0));
+
+ /*
+ * check it loaded in
+ */
+ SequenceI hmmSeq = al.getSequenceAt(0);
+ assertTrue(hmmSeq.hasHMMProfile());
+ HiddenMarkovModel hmm = hmmSeq.getHMM();
+ assertSame(hmm.getConsensusSequence(), hmmSeq);
+
+ /*
+ * save project, close windows, reload project, verify
+ */
+ File tfile = File.createTempFile("testStoreAndRecoverHmmProfile",
+ ".jvp");
+ tfile.deleteOnExit();
+ new Jalview2XML(false).saveState(tfile);
- Desktop.instance.closeAll_actionPerformed(null);
++ Desktop.getInstance().closeAll_actionPerformed(null);
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ Assert.assertNotNull(af, "Failed to reload project");
+
+ hmmSeq = al.getSequenceAt(0);
+ assertTrue(hmmSeq.hasHMMProfile());
+ assertSame(hmm.getConsensusSequence(), hmmSeq);
+ Mapping mapToHmmConsensus = (Mapping) PA.getValue(hmm,
+ "mapToHmmConsensus");
+ assertNotNull(mapToHmmConsensus);
+ assertSame(mapToHmmConsensus.getTo(), hmmSeq.getDatasetSequence());
+ }
+
+ /**
* pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
* view (JAL-3171) this test ensures we can import and merge those views
*/
@Test(groups = { "Functional" })
public void testMergeDatasetsforManyViews() throws IOException
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
// complex project - one dataset, several views on several alignments
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
@Test(groups = "Functional")
public void testPcaViewAssociation() throws IOException
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
final String PCAVIEWNAME = "With PCA";
// create a new tempfile
File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
}
// load again.
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
tempfile.getCanonicalPath(), DataSourceType.FILE);
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ JInternalFrame[] frames = Desktop.getInstance().getAllFrames();
// PCA and the tabbed alignment view should be the only two windows on the
// desktop
assertEquals(frames.length, 2,
@Test(groups = { "Functional" })
public void testStoreAndRecoverGeneLocus() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
DataSourceType.PASTE);
{
Assert.fail("Didn't save the state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
DataSourceType.FILE);
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
- import jalview.api.AlignViewportI;
+ import java.awt.Color;
+ import java.util.List;
+
+ import org.testng.annotations.BeforeClass;
+ import org.testng.annotations.BeforeMethod;
+ import org.testng.annotations.Test;
+
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
++import jalview.api.AlignViewportI;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.schemes.FeatureColour;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
- import java.awt.Color;
- import java.util.List;
-
- import org.testng.annotations.BeforeMethod;
- import org.testng.annotations.BeforeTest;
- import org.testng.annotations.Test;
-
/**
* Unit tests for feature colour determination, including but not limited to
* <ul>
*/
public class FeatureColourFinderTest
{
- private AlignViewport av;
+ private AlignViewportI av;
private SequenceI seq;
private FeatureRendererModel fr;
- @BeforeTest(alwaysRun = true)
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
// aligned column 8 is sequence position 6
git://source.jalview.org / jalview.git / commitdiff