From: gmungoc Date: Thu, 4 Jun 2015 12:40:55 +0000 (+0100) Subject: JAL-1753 ChimeraViewFrame hosts its own ProgressBar X-Git-Tag: Release_2_10_0~638 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8f9a21c422709588ddd5893904b47d01244937cd;p=jalview.git JAL-1753 ChimeraViewFrame hosts its own ProgressBar --- diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index c068728..f5b920b 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1149,6 +1149,8 @@ status.das_feature_fetching_complete = DAS Feature Fetching Complete status.fetching_db_refs = Fetching db refs status.loading_cached_pdb_entries = Loading Cached PDB Entries status.searching_for_pdb_structures = Searching for PDB Structures +status.opening_file = opening file +status.colouring_chimera = Colouring Chimera label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data label.font_too_small = Font size is too small label.error_loading_file_params = Error loading file {0} @@ -1241,4 +1243,4 @@ info.enter_search_text_here = Enter Search Text Here info.enter_search_text_to_enable = Enter Search Text to Enable info.search_in_annotation_label = Search in {0} Label info.search_in_annotation_description = Search in {0} Description -info.change_threshold_mode_to_enable = Change Threshold Mode to Enable \ No newline at end of file +info.change_threshold_mode_to_enable = Change Threshold Mode to Enable diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index 4372617..fdc7d0b 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -32,6 +32,7 @@ import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; +import java.util.Random; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; @@ -104,6 +105,8 @@ public class ChimeraViewFrame extends StructureViewerBase */ private String chimeraSessionFile = null; + private Random random = new Random(); + /** * Initialise menu options. */ @@ -304,6 +307,17 @@ public class ChimeraViewFrame extends StructureViewerBase { seq }); } + /** + * Create a helper to manage progress bar display + */ + protected void createProgressBar() + { + if (progressBar == null) + { + progressBar = new ProgressBar(statusPanel, statusBar); + } + } + protected boolean hasPdbId(String pdbId) { return jmb.hasPdbId(pdbId); @@ -312,7 +326,8 @@ public class ChimeraViewFrame extends StructureViewerBase private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) { - progressBar = ap.alignFrame; + createProgressBar(); + jmb = new JalviewChimeraBindingModel(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); addAlignmentPanel(ap); @@ -692,6 +707,8 @@ public class ChimeraViewFrame extends StructureViewerBase try { int pos = filePDBpos.get(num).intValue(); + long startTime = startProgressBar("Chimera " + + MessageManager.getString("status.opening_file")); jmb.openFile(pe); jmb.addSequence(pos, jmb.getSequence()[pos]); File fl = new File(pe.getFile()); @@ -704,6 +721,9 @@ public class ChimeraViewFrame extends StructureViewerBase } } catch (Throwable e) { + } finally + { + stopProgressBar("", startTime); } // Explicitly map to the filename used by Chimera ; // TODO: use pe.getId() instead of pe.getFile() ? @@ -765,13 +785,9 @@ public class ChimeraViewFrame extends StructureViewerBase Pdb pdbclient = new Pdb(); AlignmentI pdbseq = null; String pdbid = processingEntry.getId(); - long hdl = pdbid.hashCode() - System.currentTimeMillis(); - if (progressBar != null) - { - progressBar.setProgressBar(MessageManager.formatMessage( - "status.fetching_pdb", new Object[] - { pdbid }), hdl); - } + long hdl = startProgressBar(MessageManager.formatMessage( + "status.fetching_pdb", new Object[] + { pdbid })); try { pdbseq = pdbclient.getSequenceRecords(pdbid); @@ -780,16 +796,9 @@ public class ChimeraViewFrame extends StructureViewerBase new OOMWarning("Retrieving PDB id " + pdbid, oomerror); } finally { - if (progressBar != null) - { - progressBar - .setProgressBar( - pdbid - + " " - + MessageManager - .getString("label.state_completed"), - hdl); - } + String msg = pdbid + " " + + MessageManager.getString("label.state_completed"); + stopProgressBar(msg, hdl); } /* * If PDB data were saved and are not invalid (empty alignment), return the @@ -805,6 +814,33 @@ public class ChimeraViewFrame extends StructureViewerBase return filePath; } + /** + * Convenience method to update the progress bar if there is one. Be sure to + * call stopProgressBar with the returned handle to remove the message. + * + * @param msg + * @param handle + */ + public long startProgressBar(String msg) + { + // TODO would rather have startProgress/stopProgress as the + // IProgressIndicator interface + long tm = random.nextLong(); + if (progressBar != null) + { + progressBar.setProgressBar(msg, tm); + } + return tm; + } + + public void stopProgressBar(String msg, long handle) + { + if (progressBar != null) + { + progressBar.setProgressBar(msg, handle); + } + } + @Override public void pdbFile_actionPerformed(ActionEvent actionEvent) {