{
private static final boolean debug = false;
- /*
- * true: use REST API (recommended), false: use stdout/stdin (deprecated)
- */
- // TODO remove once definitely happy with using REST
- private static final boolean USE_REST = true;
-
private int chimeraRestPort;
private Process chimera;
modelNumbers[0], modelNumbers[1]);
currentModelsMap.put(modelNumber, newModel);
models.add(newModel);
+
+ //
// patch for Jalview - set model name in Chimera
+ //
sendChimeraCommand("setattr M name " + modelName + " #"
+ modelNumbers[0], false);
// end patch for Jalview
+
modelNumbers = null;
}
}
{
chimera = null;
currentModelsMap.clear();
- if (USE_REST)
- {
this.chimeraRestPort = 0;
- }
- else
- {
- chimeraListenerThread.requestStop();
- chimeraListenerThread = null;
- }
structureManager.clearOnChimeraExit();
}
List<String> args = new ArrayList<String>();
args.add(chimeraPath);
args.add("--start");
- args.add(USE_REST ? "RESTServer" : "ReadStdin");
+ args.add("RESTServer");
ProcessBuilder pb = new ProcessBuilder(args);
chimera = pb.start();
error = "";
workingPath = chimeraPath;
- logger.info("Starting " + chimeraPath + " with "
- + (USE_REST ? "REST API" : "stdin/stdout"));
break;
} catch (Exception e)
{
// If no error, then Chimera was launched successfully
if (error.length() == 0)
{
- if (USE_REST)
- {
- this.chimeraRestPort = getPortNumber();
- System.out.println("Chimera REST API on port " + chimeraRestPort);
- }
- else
- {
- // Initialize the listener threads
- chimeraListenerThread = new ListenerThreads(chimera,
- structureManager);
- chimeraListenerThread.start();
- }
+ this.chimeraRestPort = getPortNumber();
+ System.out.println("Chimera REST API started on port "
+ + chimeraRestPort);
// structureManager.initChimTable();
structureManager.setChimeraPathProperty(workingPath);
// TODO: [Optional] Check Chimera version and show a warning if below 1.8
} catch (InterruptedException q)
{
}
- ;
}
busy = true;
long startTime = System.currentTimeMillis();
try
{
- if (USE_REST)
- {
- return sendRestCommand(command);
- }
- else
- {
- return sendStdinCommand(command, reply);
- }
+ return sendRestCommand(command);
} finally
{
+ /*
+ * Make sure busy flag is reset come what may!
+ */
busy = false;
if (debug)
{
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.Hashtable;
public class PDBEntry
{
*
* @see java.lang.Object#equals(java.lang.Object)
*/
+ @Override
public boolean equals(Object obj)
{
if (obj == null || !(obj instanceof PDBEntry))
return false;
}
if (obj == this)
+ {
return true;
+ }
PDBEntry o = (PDBEntry) obj;
return (file == o.file || (file != null && o.file != null && o.file
.equals(file)))
.equals(o.properties)));
}
+ /**
+ * Default constructor
+ */
public PDBEntry()
{
}
+ /**
+ * Constructor given file path and PDB id.
+ *
+ * @param filePath
+ */
+ public PDBEntry(String filePath, String pdbId)
+ {
+ this.file = filePath;
+ this.id = pdbId;
+ }
+
+ /**
+ * Copy constructor.
+ *
+ * @param entry
+ */
public PDBEntry(PDBEntry entry)
{
file = entry.file;
--- /dev/null
+package jalview.datamodel;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * A data bean to hold stored data about a structure viewer.
+ */
+public class ViewerData
+{
+ private int x;
+
+ private int y;
+
+ private int width;
+
+ private int height;
+
+ private boolean alignWithPanel;
+
+ private boolean colourWithAlignPanel;
+
+ private boolean colourByViewer;
+
+ private String stateData = "";
+
+ private Map<File, StructureData> fileData = new HashMap<File, StructureData>();
+
+ public class StructureData
+ {
+ private String filePath;
+
+ private String pdbId;
+
+ private List<SequenceI> seqList;
+
+ // TODO and possibly a list of chains?
+
+ /**
+ * Constructor given structure file path and id.
+ *
+ * @param pdbFile
+ * @param id
+ */
+ public StructureData(String pdbFile, String id)
+ {
+ this.filePath = pdbFile;
+ this.pdbId = id;
+ this.seqList = new ArrayList<SequenceI>();
+ }
+
+ public String getFilePath()
+ {
+ return filePath;
+ }
+
+ protected void setFilePath(String filePath)
+ {
+ this.filePath = filePath;
+ }
+
+ public String getPdbId()
+ {
+ return pdbId;
+ }
+
+ protected void setPdbId(String pdbId)
+ {
+ this.pdbId = pdbId;
+ }
+
+ public List<SequenceI> getSeqList()
+ {
+ return seqList;
+ }
+
+ protected void setSeqList(List<SequenceI> seqList)
+ {
+ this.seqList = seqList;
+ }
+ }
+
+ public ViewerData(int x, int y, int width, int height,
+ boolean alignWithPanel, boolean colourWithAlignPanel,
+ boolean colourByViewer)
+ {
+ this.x = x;
+ this.y = y;
+ this.width = width;
+ this.height = height;
+ this.alignWithPanel = alignWithPanel;
+ this.colourWithAlignPanel = colourWithAlignPanel;
+ this.colourByViewer = colourByViewer;
+ }
+
+ public int getX()
+ {
+ return x;
+ }
+
+ protected void setX(int x)
+ {
+ this.x = x;
+ }
+
+ public int getY()
+ {
+ return y;
+ }
+
+ protected void setY(int y)
+ {
+ this.y = y;
+ }
+
+ public int getWidth()
+ {
+ return width;
+ }
+
+ protected void setWidth(int width)
+ {
+ this.width = width;
+ }
+
+ public int getHeight()
+ {
+ return height;
+ }
+
+ public void setHeight(int height)
+ {
+ this.height = height;
+ }
+
+ public boolean isAlignWithPanel()
+ {
+ return alignWithPanel;
+ }
+
+ public void setAlignWithPanel(boolean alignWithPanel)
+ {
+ this.alignWithPanel = alignWithPanel;
+ }
+
+ public boolean isColourWithAlignPanel()
+ {
+ return colourWithAlignPanel;
+ }
+
+ public void setColourWithAlignPanel(boolean colourWithAlignPanel)
+ {
+ this.colourWithAlignPanel = colourWithAlignPanel;
+ }
+
+ public boolean isColourByViewer()
+ {
+ return colourByViewer;
+ }
+
+ public void setColourByViewer(boolean colourByViewer)
+ {
+ this.colourByViewer = colourByViewer;
+ }
+
+ public String getStateData()
+ {
+ return stateData;
+ }
+
+ public void setStateData(String stateData)
+ {
+ this.stateData = stateData;
+ }
+
+ public Map<File, StructureData> getFileData()
+ {
+ return fileData;
+ }
+
+ protected void setFileData(Map<File, StructureData> fileData)
+ {
+ this.fileData = fileData;
+ }
+
+}
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
import jalview.util.MessageManager;
import java.awt.Color;
-import java.io.File;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashMap;
private ChimeraManager viewer;
- /**
+ /*
* set if chimera state is being restored from some source - instructs binding
* not to apply default display style when structure set is updated for first
* time.
*/
private boolean loadingFromArchive = false;
- /**
- * second flag to indicate if the Chimera viewer should ignore sequence
- * colouring events from the structure manager because the GUI is still
- * setting up
+ /*
+ * flag to indicate if the Chimera viewer should ignore sequence colouring
+ * events from the structure manager because the GUI is still setting up
*/
private boolean loadingFinished = true;
- /**
+ /*
* state flag used to check if the Chimera viewer's paint method can be called
*/
private boolean finishedInit = false;
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
- boolean allChainsSelected = false;
-
- /**
- * when true, try to search the associated datamodel for sequences that are
- * associated with any unknown structures in the Chimera view.
- */
- private boolean associateNewStructs = false;
+ private List<String> atomsPicked = new ArrayList<String>();
- List<String> atomsPicked = new ArrayList<String>();
-
- public List<String> chainNames;
+ private List<String> chainNames;
private Map<String, String> chainFile;
- StringBuffer eval = new StringBuffer();
+ private StringBuffer eval = new StringBuffer();
public String fileLoadingError;
- private Map<String, List<ChimeraModel>> chimmaps = new LinkedHashMap<String, List<ChimeraModel>>();
-
- private List<String> mdlToFile = new ArrayList<String>();
+ /*
+ * Map of ChimeraModel objects keyed by PDB full local file name
+ */
+ private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
- /**
+ /*
* the default or current model displayed if the model cannot be identified
* from the selection message
*/
- int frameNo = 0;
+ private int frameNo = 0;
- String lastCommand;
+ private String lastCommand;
- String lastMessage;
+ private String lastMessage;
- boolean loadedInline;
+ private boolean loadedInline;
+ /**
+ * Open a PDB structure file in Chimera and set up mappings from Jalview.
+ *
+ * We check if the PDB model id is already loaded in Chimera, if so don't
+ * reopen it. This is the case if Chimera has opened a saved session file.
+ *
+ * @param pe
+ * @return
+ */
public boolean openFile(PDBEntry pe)
{
String file = pe.getFile();
try
{
+ List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
List<ChimeraModel> oldList = viewer.getModelList();
- viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
- List<ChimeraModel> newList = viewer.getModelList();
- if (oldList.size() < newList.size())
+ boolean alreadyOpen = false;
+
+ /*
+ * If Chimera already has this model, don't reopen it, but do remap it.
+ */
+ for (ChimeraModel open : oldList)
{
- while (oldList.size() > 0)
+ if (open.getModelName().equals(pe.getId()))
{
- oldList.remove(0);
- newList.remove(0);
- }
- chimmaps.put(file, newList);
- for (ChimeraModel cm : newList)
- {
- while (mdlToFile.size() < 1 + cm.getModelNumber())
- {
- mdlToFile.add(new String(""));
- }
- mdlToFile.set(cm.getModelNumber(), file);
+ alreadyOpen = true;
+ modelsToMap.add(open);
}
+ }
- File fl = new File(file);
- String protocol = AppletFormatAdapter.URL;
- try
- {
- if (fl.exists())
- {
- protocol = AppletFormatAdapter.FILE;
- }
- } catch (Exception e)
- {
- } catch (Error e)
- {
- }
- // Explicitly map to the filename used by Chimera ;
- // pdbentry[pe].getFile(), protocol);
+ /*
+ * If Chimera doesn't yet have this model, ask it to open it, and retrieve
+ * the model names added by Chimera.
+ */
+ if (!alreadyOpen)
+ {
+ viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
+ modelsToMap = viewer.getModelList();
+ modelsToMap.removeAll(oldList);
+ }
+
+ chimeraMaps.put(file, modelsToMap);
- if (getSsm() != null)
+ if (getSsm() != null)
+ {
+ getSsm().addStructureViewerListener(this);
+ // ssm.addSelectionListener(this);
+ FeatureRenderer fr = getFeatureRenderer(null);
+ if (fr != null)
{
- getSsm().addStructureViewerListener(this);
- // ssm.addSelectionListener(this);
- FeatureRenderer fr = getFeatureRenderer(null);
- if (fr != null)
- {
- fr.featuresAdded();
- }
- refreshGUI();
+ fr.featuresAdded();
}
- return true;
+ refreshGUI();
}
+ return true;
} catch (Exception q)
{
log("Exception when trying to open model " + file + "\n"
{
if (!viewer.isChimeraLaunched())
{
- viewer.launchChimera(csm.getChimeraPaths());
+ viewer.launchChimera(StructureManager.getChimeraPaths());
}
if (!viewer.isChimeraLaunched())
{
}
/**
- * Send a command to Chimera, and optionally log any responses.
+ * Send a command to Chimera, launching it first if necessary, and optionally
+ * log any responses.
*
* @param command
* @param logResponse
checkLaunched();
if (lastCommand == null || !lastCommand.equals(command))
{
-// Thread t = new Thread(new Runnable()
-// {
-// @Override
-// public void run()
-// {
// trim command or it may never find a match in the replyLog!!
lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
if (debug && logResponse)
- {
- log("Response from command ('" + command + "') was:\n"
- + lastReply);
- }
-// }
-// });
- // TODO - use j7/8 thread management
-// try
-// {
-// t.join();
-// } catch (InterruptedException foo)
-// {
-// }
-// ;
+ {
+ log("Response from command ('" + command + "') was:\n" + lastReply);
+ }
}
viewerCommandHistory(true);
lastCommand = command;
// // System.arraycopy(mset, 0, modelFileNames, 0, j);
// }
- return chimmaps.keySet().toArray(
- modelFileNames = new String[chimmaps.size()]);
+ return chimeraMaps.keySet().toArray(
+ modelFileNames = new String[chimeraMaps.size()]);
}
/**
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbfile)
{
- List<ChimeraModel> cms = chimmaps.get(pdbfile);
+ List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
if (cms != null)
{
int mdlNum = cms.get(0).getModelNumber();
return true;
}
+ public boolean isFinishedInit()
+ {
+ return finishedInit;
+ }
+
+ public void setFinishedInit(boolean finishedInit)
+ {
+ this.finishedInit = finishedInit;
+ }
+
+ public List<String> getChainNames()
+ {
+ return chainNames;
+ }
+
}
PDBEntry[] pdbentrys = new PDBEntry[files.length];
for (int i = 0; i < pdbentrys.length; i++)
{
- PDBEntry pdbentry = new PDBEntry();
- pdbentry.setFile(files[i]);
- pdbentry.setId(ids[i]);
+ PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
pdbentrys[i] = pdbentry;
}
// / TODO: check if protocol is needed to be set, and if chains are
seqColour.setSelected(false);
viewerColour.setSelected(true);
}
- if (usetoColour)
+ else if (usetoColour)
{
useAlignmentPanelForColourbyseq(ap);
jmb.setColourBySequence(true);
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
-import jalview.gui.Jalview2XML.ViewerData;
import jalview.io.AppletFormatAdapter;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
private Thread worker = null;
/*
- * Path to Chimera session file - set in saveSession()
+ * Path to Chimera session file. This is set when an open Jalview/Chimera
+ * session is saved, or on restore from a Jalview project (if it holds the
+ * filename of any saved Chimera sessions).
*/
- private String chimeraSessionFile = "";
+ private String chimeraSessionFile = null;
/**
* Initialise menu options.
jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
initMenus();
- worker = null;
- {
- addingStructures = false;
- worker = new Thread(this);
- worker.start();
- }
+
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
}
/**
- * Create a new viewer from saved session state data.
+ * Create a new viewer from saved session state data including Chimera session
+ * file.
+ *
+ * @param chimeraSession
*
- * @param viewerData
- * @param af
+ * @param alignPanel
+ * @param pdbArray
+ * @param seqsArray
+ * @param colourByChimera
+ * @param colourBySequence
*/
- public ChimeraViewFrame(ViewerData viewerData, AlignFrame af)
+ public ChimeraViewFrame(String chimeraSession, AlignmentPanel alignPanel,
+ PDBEntry[] pdbArray,
+ SequenceI[][] seqsArray, boolean colourByChimera,
+ boolean colourBySequence)
{
super();
- String chimeraSessionFile = viewerData.stateData;
- openNewChimera(af.alignPanel, new PDBEntry[]
- {}, new SequenceI[][]
- {});
- initChimera("open " + chimeraSessionFile);
- // TODO restore mappings
+ this.chimeraSessionFile = chimeraSession;
+ openNewChimera(alignPanel, pdbArray, seqsArray);
+ if (colourByChimera)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
+ }
+ else if (colourBySequence)
+ {
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
+ }
}
/**
return result;
}
- void initChimera(String command)
+ /**
+ * Launch Chimera. If we have a chimera session file name, send Chimera the
+ * command to open its saved session file.
+ */
+ void initChimera()
{
jmb.setFinishedInit(false);
- // TODO: consider waiting until the structure/view is fully loaded before
- // displaying
jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
getBounds().width, getBounds().height);
- if (command == null)
+
+ /*
+ * Pass an empty 'command' to launch Chimera
+ */
+ jmb.evalStateCommand("", false);
+
+ if (this.chimeraSessionFile != null)
{
- command = "";
+ boolean opened = jmb.openSession(chimeraSessionFile);
+ if (!opened)
+ {
+ System.err
+ .println("An error occurred opening Chimera session file "
+ + chimeraSessionFile);
+ }
}
- jmb.evalStateCommand(command, false);
jmb.setFinishedInit(true);
}
{
try
{
- initChimera("");
+ initChimera();
} catch (Exception ex)
{
Cache.log.error("Couldn't open Chimera viewer!", ex);
repaint();
return;
}
- setChainMenuItems(jmb.chainNames);
+ setChainMenuItems(jmb.getChainNames());
this.setTitle(jmb.getViewerTitle("Chimera", true));
if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.ViewerData;
+import jalview.datamodel.ViewerData.StructureData;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.Alcodon;
import jalview.schemabinding.version2.AlcodonFrame;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
*/
public class Jalview2XML
{
-
- /**
- * A data bean to hold stored data about a structure viewer.
- */
- public class ViewerData
- {
-
- private int x;
-
- private int y;
-
- private int width;
-
- private int height;
-
- public boolean alignWithPanel;
-
- public boolean colourWithAlignPanel;
-
- public boolean colourByViewer;
-
- String stateData = "";
-
- // todo: java bean in place of Object []
- private Map<File, Object[]> fileData = new HashMap<File, Object[]>();
-
- public ViewerData(int x, int y, int width, int height,
- boolean alignWithPanel, boolean colourWithAlignPanel,
- boolean colourByViewer)
- {
- this.x = x;
- this.y = y;
- this.width = width;
- this.height = height;
- this.alignWithPanel = alignWithPanel;
- this.colourWithAlignPanel = colourWithAlignPanel;
- this.colourByViewer = colourByViewer;
- }
-
- }
-
/*
* SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
* of sequence objects are created.
protected void loadStructures(jarInputStreamProvider jprovider,
JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
{
- // run through all PDB ids on the alignment, and collect mappings between
- // jmol view ids and all sequences referring to it
- Map<String, ViewerData> jmolViewIds = new HashMap<String, ViewerData>();
+ /*
+ * Run through all PDB ids on the alignment, and collect mappings between
+ * distinct view ids and all sequences referring to that view.
+ */
+ Map<String, ViewerData> structureViewers = new LinkedHashMap<String, ViewerData>();
for (int i = 0; i < jseqs.length; i++)
{
sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
+ "," + height;
}
- if (!jmolViewIds.containsKey(sviewid))
+ if (!structureViewers.containsKey(sviewid))
{
- jmolViewIds.put(sviewid, new ViewerData(x, y, width, height,
+ structureViewers.put(sviewid, new ViewerData(x, y, width, height,
false, false, true));
// Legacy pre-2.7 conversion JAL-823 :
// do not assume any view has to be linked for colour by
// file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
// seqs_file 2}, boolean[] {
// linkAlignPanel,superposeWithAlignpanel}} from hash
- ViewerData jmoldat = jmolViewIds.get(sviewid);
- jmoldat.alignWithPanel |= structureState
- .hasAlignwithAlignPanel() ? structureState.getAlignwithAlignPanel() : false;
- // never colour by linked panel if not specified
- jmoldat.colourWithAlignPanel |= structureState
- .hasColourwithAlignPanel() ? structureState.getColourwithAlignPanel()
- : false;
- // default for pre-2.7 projects is that Jmol colouring is enabled
- jmoldat.colourByViewer &= structureState
+ ViewerData jmoldat = structureViewers.get(sviewid);
+ jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
+ | (structureState.hasAlignwithAlignPanel() ? structureState
+ .getAlignwithAlignPanel() : false));
+
+ /*
+ * Default colour by linked panel to false if not specified (e.g.
+ * for pre-2.7 projects)
+ */
+ boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
+ colourWithAlignPanel |= (structureState
+ .hasColourwithAlignPanel() ? structureState
+ .getColourwithAlignPanel() : false);
+ jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
+
+ /*
+ * Default colour by viewer to true if not specified (e.g. for
+ * pre-2.7 projects)
+ */
+ boolean colourByViewer = jmoldat.isColourByViewer();
+ colourByViewer &= structureState
.hasColourByJmol() ? structureState
.getColourByJmol() : true;
+ jmoldat.setColourByViewer(colourByViewer);
- if (jmoldat.stateData.length() < structureState.getContent()
- .length())
+ if (jmoldat.getStateData().length() < structureState
+ .getContent().length())
{
{
- jmoldat.stateData = structureState.getContent();
+ jmoldat.setStateData(structureState.getContent());
}
}
if (ids[p].getFile() != null)
{
File mapkey = new File(ids[p].getFile());
- Object[] seqstrmaps = jmoldat.fileData.get(mapkey);
+ StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
if (seqstrmaps == null)
{
- jmoldat.fileData.put(mapkey,
- seqstrmaps = new Object[]
- { pdbFile, ids[p].getId(), new Vector(),
- new Vector() });
+ jmoldat.getFileData().put(
+ mapkey,
+ seqstrmaps = jmoldat.new StructureData(pdbFile,
+ ids[p].getId()));
}
- if (!((Vector) seqstrmaps[2]).contains(seq))
+ if (!seqstrmaps.getSeqList().contains(seq))
{
- ((Vector) seqstrmaps[2]).addElement(seq);
- // ((Vector)seqstrmaps[3]).addElement(n) :
- // in principle, chains
- // should be stored here : do we need to
- // TODO: store and recover seq/pdb_id :
- // chain mappings
+ seqstrmaps.getSeqList().add(seq);
+ // TODO and chains?
}
}
else
}
}
// Instantiate the associated structure views
- for (Entry<String, ViewerData> entry : jmolViewIds.entrySet())
+ for (Entry<String, ViewerData> entry : structureViewers.entrySet())
{
createOrLinkStructureViewer(entry, af, ap);
}
* Pending an XML element for ViewerType, just check if stateData contains
* "chimera" (part of the chimera session filename).
*/
- if (svattrib.stateData.indexOf("chimera") > -1)
+ if (svattrib.getStateData().indexOf("chimera") > -1)
{
createChimeraViewer(viewerData, af);
}
AlignFrame af)
{
final ViewerData data = viewerData.getValue();
- String chimeraSession = data.stateData;
- List<String> pdbfilenames = new ArrayList<String>();
- List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
- List<String> pdbids = new ArrayList<String>();
+ String chimeraSession = data.getStateData();
if (new File(chimeraSession).exists())
{
- Set<Entry<File, Object[]>> fileData = data.fileData.entrySet();
+ Set<Entry<File, StructureData>> fileData = data.getFileData()
+ .entrySet();
List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
- for (Entry<File, Object[]> pdb : fileData)
- {
- String filePath = (String) pdb.getValue()[0];
- String pdbId = (String) pdb.getValue()[1];
- final Vector seqList = (Vector) pdb.getValue()[2];
- PDBEntry pdbentry = new PDBEntry();
- pdbentry.setFile(filePath);
- pdbentry.setId(pdbId);
- pdbs.add(pdbentry);
- SequenceI[] seqs = new SequenceI[seqList.size()];
- seqList.copyInto(seqs);
+ for (Entry<File, StructureData> pdb : fileData)
+ {
+ String filePath = pdb.getValue().getFilePath();
+ String pdbId = pdb.getValue().getPdbId();
+ pdbs.add(new PDBEntry(filePath, pdbId));
+ final List<SequenceI> seqList = pdb.getValue().getSeqList();
+ SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
allseqs.add(seqs);
}
+ boolean colourByChimera = data.isColourByViewer();
+ boolean colourBySequence = data.isColourWithAlignPanel();
+
// TODO can/should this be done via StructureViewer (like Jmol)?
final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs
.size()]);
final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs.size()][]);
- ChimeraViewFrame cvf = // new ChimeraViewFrame(data, af);
- new ChimeraViewFrame(af.alignPanel, pdbArray, seqsArray);
+ new ChimeraViewFrame(chimeraSession, af.alignPanel, pdbArray,
+ seqsArray,
+ colourByChimera, colourBySequence);
}
else
{
final Entry<String, ViewerData> viewerData, AlignFrame af)
{
final ViewerData svattrib = viewerData.getValue();
- String state = svattrib.stateData;
+ String state = svattrib.getStateData();
List<String> pdbfilenames = new ArrayList<String>();
List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
List<String> pdbids = new ArrayList<String>();
StringBuilder newFileLoc = new StringBuilder(64);
int cp = 0, ncp, ecp;
- Map<File, Object[]> oldFiles = svattrib.fileData;
+ Map<File, StructureData> oldFiles = svattrib.getFileData();
while ((ncp = state.indexOf("load ", cp)) > -1)
{
do
// have to normalize filename - since Jmol and jalview do
// filename
// translation differently.
- Object[] filedat = oldFiles.get(new File(oldfilenam));
- newFileLoc.append(Platform.escapeString((String) filedat[0]));
- pdbfilenames.add((String) filedat[0]);
- pdbids.add((String) filedat[1]);
- seqmaps.add(((Vector<SequenceI>) filedat[2])
+ StructureData filedat = oldFiles.get(new File(oldfilenam));
+ newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+ pdbfilenames.add(filedat.getFilePath());
+ pdbids.add(filedat.getPdbId());
+ seqmaps.add(filedat.getSeqList()
.toArray(new SequenceI[0]));
newFileLoc.append("\"");
cp = ecp + 1; // advance beyond last \" and set cursor so we can
{
// add this and any other pdb files that should be present in
// the viewer
- Object[] filedat = oldFiles.get(id);
- String nfilename;
- newFileLoc.append(((String) filedat[0]));
- pdbfilenames.add((String) filedat[0]);
- pdbids.add((String) filedat[1]);
- seqmaps.add(((Vector<SequenceI>) filedat[2])
+ StructureData filedat = oldFiles.get(id);
+ newFileLoc.append(filedat.getFilePath());
+ pdbfilenames.add(filedat.getFilePath());
+ pdbids.add(filedat.getPdbId());
+ seqmaps.add(filedat.getSeqList()
.toArray(new SequenceI[0]));
newFileLoc.append(" \"");
- newFileLoc.append((String) filedat[0]);
+ newFileLoc.append(filedat.getFilePath());
newFileLoc.append("\"");
}
final String fileloc = newFileLoc.toString();
final String sviewid = viewerData.getKey();
final AlignFrame alf = af;
- final java.awt.Rectangle rect = new java.awt.Rectangle(svattrib.x,
- svattrib.y, svattrib.width, svattrib.height);
+ final Rectangle rect = new Rectangle(svattrib.getX(),
+ svattrib.getY(), svattrib.getWidth(), svattrib.getHeight());
try
{
javax.swing.SwingUtilities.invokeAndWait(new Runnable()
/*
* Otherwise test for matching position and size of viewer frame
*/
- else if (frame.getX() == svattrib.x && frame.getY() == svattrib.y
- && frame.getHeight() == svattrib.height
- && frame.getWidth() == svattrib.width)
+ else if (frame.getX() == svattrib.getX()
+ && frame.getY() == svattrib.getY()
+ && frame.getHeight() == svattrib.getHeight()
+ && frame.getWidth() == svattrib.getWidth())
{
comp = (AppJmol) frame;
// todo: break?
// NOTE: if the jalview project is part of a shared session then
// view synchronization should/could be done here.
- final boolean useinViewerSuperpos = svattrib.alignWithPanel;
- final boolean usetoColourbyseq = svattrib.colourWithAlignPanel;
- final boolean viewerColouring = svattrib.colourByViewer;
- Map<File, Object[]> oldFiles = svattrib.fileData;
+ final boolean useinViewerSuperpos = svattrib.isAlignWithPanel();
+ final boolean usetoColourbyseq = svattrib.isColourWithAlignPanel();
+ final boolean viewerColouring = svattrib.isColourByViewer();
+ Map<File, StructureData> oldFiles = svattrib.getFileData();
/*
* Add mapping for sequences in this view to an already open viewer
{
// add this and any other pdb files that should be present in the
// viewer
- Object[] filedat = oldFiles.get(id);
- String pdbFile = (String) filedat[0];
- SequenceI[] seq = ((Vector<SequenceI>) filedat[2])
- .toArray(new SequenceI[0]);
- binding
- .getSsm()
- .setMapping(seq, null, pdbFile,
+ StructureData filedat = oldFiles.get(id);
+ String pdbFile = filedat.getFilePath();
+ SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
+ binding.getSsm().setMapping(seq, null, pdbFile,
jalview.io.AppletFormatAdapter.FILE);
binding.addSequenceForStructFile(pdbFile, seq);
}
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.gui.Jalview2XML.ViewerData;
+import jalview.datamodel.ViewerData;
import jalview.structure.StructureSelectionManager;
import java.awt.Rectangle;
AlignmentPanel alignPanel, ViewerData viewerData, String fileloc,
Rectangle rect, String vid)
{
- final boolean useinViewerSuperpos = viewerData.alignWithPanel;
- final boolean usetoColourbyseq = viewerData.colourWithAlignPanel;
- final boolean viewerColouring = viewerData.colourByViewer;
+ final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
+ final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
+ final boolean viewerColouring = viewerData.isColourByViewer();
JalviewStructureDisplayI sview = null;
switch (type)
{
case JMOL:
- sview = new AppJmol(pdbf, id, sq, alignPanel, useinViewerSuperpos,
- usetoColourbyseq, viewerColouring, fileloc, rect, vid);
+ sview = new AppJmol(pdbf, id, sq, alignPanel, usetoColourbyseq,
+ useinViewerSuperpos, viewerColouring, fileloc, rect, vid);
break;
case CHIMERA:
Cache.log.error("Unsupported structure viewer type "
git://source.jalview.org / jalview.git / commitdiff