package jalview.bin;
import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Locale;
import java.util.Map;
import jalview.analysis.AlignmentUtils;
+import jalview.api.AlignmentViewPanel;
import jalview.bin.ArgParser.Arg;
import jalview.bin.ArgParser.ArgValues;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
+import jalview.gui.StructureChooser;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormatException;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.ws.dbsources.EBIAlfaFold;
public class Commands
{
{
argParser = ap;
headless = h;
- for (String id : argParser.linkedIds())
+ if (argParser != null && argParser.linkedIds() != null)
{
- Commands cmds = new Commands();
- if (id == null)
+ for (String id : argParser.linkedIds())
{
- cmds.processUnlinked(id);
- }
- else
- {
- cmds.processLinked(id);
+ Commands cmds = new Commands();
+ if (id == null)
+ {
+ cmds.processUnlinked(id);
+ }
+ else
+ {
+ cmds.processLinked(id);
+ }
}
}
}
protected void processLinked(String id)
{
Map<Arg, ArgValues> m = argParser.linkedArgs(id);
- FileLoader fileLoader = new FileLoader(!headless);
/*
// script to execute after all loading is completed one way or another
{
if (openFile == null)
continue OPEN;
- Console.debug("********** id = " + id + ", openFile = " + openFile);
if (first)
{
af = afMap.get(id);
if (af == null)
{
+ // get kind of temperature factor annotation
+ AlignmentAnnotation.TFType tempfacType = null;
+ if ((m.get(Arg.NOTEMPFAC) == null
+ || !m.get(Arg.NOTEMPFAC).getBoolean())
+ && m.get(Arg.TEMPFAC) != null)
+ {
+ try
+ {
+ tempfacType = AlignmentAnnotation.TFType
+ .valueOf(m.get(Arg.TEMPFAC).getValue()
+ .toUpperCase(Locale.ROOT));
+ Console.debug("Obtained Temperature Factor type of '"
+ + tempfacType + "'");
+ } catch (IllegalArgumentException e)
+ {
+ StringBuilder sb = new StringBuilder().append("Cannot set --")
+ .append(Arg.TEMPFAC.getName()).append(" to '")
+ .append(tempfacType)
+ .append("', ignoring. Valid values are: ");
+ Iterator<AlignmentAnnotation.TFType> it = Arrays
+ .stream(AlignmentAnnotation.TFType.values())
+ .iterator();
+ while (it.hasNext())
+ {
+ sb.append(it.next().toString().toLowerCase(Locale.ROOT));
+ if (it.hasNext())
+ sb.append(", ");
+ }
+ Console.warn(sb.toString());
+ }
+ }
+
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
- af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
- format);
+ FileLoader fileLoader = new FileLoader(!headless);
+ af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format,
+ tempfacType);
+
+ // wrap alignment?
+ if (m.get(Arg.WRAP) != null && m.get(Arg.WRAP).getBoolean())
+ {
+ af.getCurrentView().setWrapAlignment(true);
+ }
+
+ // change alignment frame title
if (m.get(Arg.TITLE) != null)
af.setTitle(m.get(Arg.TITLE).getValue());
+
+ // show secondary structure annotations?
if (m.get(Arg.SSANNOTATION) != null
&& !m.get(Arg.SSANNOTATION).getBoolean())
{
Collections.singleton("Secondary Structure"), null,
false, false);
}
+
+ // show temperature factor annotations?
if (m.get(Arg.NOTEMPFAC) != null
&& m.get(Arg.NOTEMPFAC).getBoolean())
{
// do this better (annotation types?)
+ List<String> hideThese = new ArrayList<>();
+ hideThese.add("Temperature Factor");
+ hideThese.add(MessageManager
+ .getString("label.alphafold_reliability"));
AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(),
- Collections.singleton("Temperature Factor"), null,
- false, false);
- AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(),
- Collections.singleton("Alphafold Reliability"), null,
+ af.getCurrentView().getAlignment(), hideThese, null,
false, false);
}
+ else
+ {
+ if (m.get(Arg.TEMPFAC_LABEL) != null)
+ {
+ AlignmentAnnotation aa = AlignmentUtils
+ .getFirstSequenceAnnotationOfType(
+ af.getCurrentView().getAlignment(),
+ AlignmentAnnotation.LINE_GRAPH);
+ if (aa != null)
+ {
+ aa.label = m.get(Arg.TEMPFAC_LABEL).getValue();
+ }
+ }
+ }
// store the AlignFrame for this id
afMap.put(id, af);
}
}
+
+ // load a pAE file if given
+ if (m.get(Arg.PAEMATRIX) != null)
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ for (String val : m.get(Arg.PAEMATRIX).getValues())
+ {
+ SubId subId = new SubId(val);
+ File paeFile = new File(subId.content);
+ EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+ paeFile, subId.index,
+ "id".equals(subId.keyName) ? subId.keyValue : null);
+ // required to readjust the height and position of the pAE
+ // annotation
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ ap.adjustAnnotationHeight();
+ }
+ }
+ }
+ }
+
+ // open the structure (from same PDB file or given PDBfile)
+ if (m.get(Arg.NOSTRUCTURE) == null
+ || !m.get(Arg.NOQUESTIONNAIRE).getBoolean())
+ {
+ AlignFrame af = afMap.get(id);
+ if (m.get(Arg.STRUCTURE) != null)
+ {
+ STRUCTURE: for (String val : m.get(Arg.STRUCTURE).getValues())
+ {
+ SubId subId = new SubId(val);
+ SequenceI seq = getSpecifiedSequence(af, subId);
+ if (seq == null)
+ {
+ Console.warn("Could not find sequence for argument --"
+ + Arg.STRUCTURE + "=" + val);
+ break STRUCTURE;
+ }
+ File structureFile = null;
+ if (subId.content != null && subId.content.length() != 0)
+ {
+ structureFile = new File(subId.content);
+ Console.debug("Using structure file (from argument) '"
+ + structureFile.getAbsolutePath() + "'");
+ }
+ /* THIS DOESN'T WORK */
+ else if (seq.getAllPDBEntries() != null
+ && seq.getAllPDBEntries().size() > 0)
+ {
+ structureFile = new File(
+ seq.getAllPDBEntries().elementAt(0).getFile());
+ Console.debug("Using structure file (from sequence) '"
+ + structureFile.getAbsolutePath() + "'");
+ }
+
+ if (structureFile == null)
+ {
+ Console.warn("Not provided structure file with '" + val + "'");
+ continue STRUCTURE;
+ }
+
+ if (!structureFile.exists())
+ {
+ Console.warn("Structure file '"
+ + structureFile.getAbsoluteFile() + "' not found.");
+ continue STRUCTURE;
+ }
+
+ Console.debug("Using structure file "
+ + structureFile.getAbsolutePath());
+
+ // open structure view
+ AlignmentPanel ap = af.alignPanel;
+ StructureChooser.openStructureFileForSequence(ap, seq,
+ structureFile);
+ }
+ }
+ }
+ }
+
+ private SequenceI getSpecifiedSequence(AlignFrame af, SubId subId)
+ {
+ SequenceI seq = null;
+ SequenceI[] sequences = af.getCurrentView().getAlignment()
+ .getSequencesArray();
+ if (-1 < subId.index && subId.index < sequences.length)
+ {
+ seq = sequences[subId.index];
+ }
+ else if ("id".equals(subId.keyName))
+ {
+ for (SequenceI s : sequences)
+ {
+ if (s.getDisplayId(false).equals(subId.keyValue))
+ {
+ seq = s;
+ break;
+ }
+ }
+ }
+ return seq;
}
+ /**
+ * A helper class to parse a string of the possible forms "content"
+ * "[index]content", "[keyName=keyValue]content" and return the integer index,
+ * the strings keyName and keyValue, and the content after the square brackets
+ * (if present). Values not set will be -1 or null.
+ */
+ protected class SubId
+ {
+ protected int index = 0;
+
+ protected String keyName = null;
+
+ protected String keyValue = null;
+
+ protected String content = null;
+
+ protected SubId(String item)
+ {
+ if (item.indexOf('[') == 0 && item.indexOf(']') > 1)
+ {
+ int openBracket = item.indexOf('[');
+ int closeBracket = item.indexOf(']');
+ String indexString = item.substring(openBracket + 1, closeBracket);
+ this.content = item.substring(closeBracket + 1);
+ int equals = indexString.indexOf('=');
+ if (equals > -1)
+ {
+ this.keyName = indexString.substring(0, equals);
+ this.keyValue = indexString.substring(equals + 1);
+ this.index = -1;
+ }
+ else
+ {
+ try
+ {
+ this.index = Integer.parseInt(indexString);
+ } catch (NumberFormatException e)
+ {
+ Console.warn("Failed to obtain sequenced id or index from '"
+ + item + "'. Setting index=0 and using content='"
+ + content + "'.");
+ }
+ }
+ }
+ else
+ {
+ this.content = item;
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff