--open=./examples/test_fab41.result/sample.a2m
---colour=clustal
+--colour=gecos:flower
--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb
---paematrix=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json
+--paematrix=[label=pAE R1-M3]./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json
--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb
---paematrix=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4_scores.json
+--paematrix=[label=pAE R2-M4]./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4_scores.json
--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb
---paematrix=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2_scores.json
+--paematrix=[label=pAE R3-M2]./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2_scores.json
--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5.pdb
---paematrix=./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5_scores.json
+--paematrix=[label=pAE R4-M5]./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5_scores.json
--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1.pdb
---paematrix=./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1_scores.json
+--paematrix=[label=pAE R5-M1]./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1_scores.json
--image=output1.html
---close
import jalview.bin.argparser.Arg;
import jalview.bin.argparser.ArgParser;
import jalview.bin.argparser.ArgValue;
+import jalview.bin.argparser.ArgValues;
import jalview.bin.argparser.ArgValuesMap;
import jalview.bin.argparser.SubVals;
import jalview.datamodel.AlignmentAnnotation;
{
String val = av.getValue();
SubVals subVals = ArgParser.getSubVals(val);
+ String paeLabel = subVals.get("label");
File paeFile = new File(subVals.getContent());
String paePath = null;
try
Console.warn(
"Problem with the PAE file path: '" + paePath + "'");
}
- String structId = subVals.get("structid");
+ String structid = null;
+ String structfile = null;
+ String seqid = null;
if (subVals.notSet())
{
- // take structid from pdbfilename
+ ArgValue likelyStructure = avm
+ .getClosestPreviousArgValueOfArg(av, Arg.STRUCTURE);
+ if (likelyStructure != null)
+ {
+ SubVals sv = likelyStructure.getSubVals();
+ if (sv != null && sv.has(ArgValues.ID))
+ {
+ structid = sv.get(ArgValues.ID);
+ }
+ else
+ {
+ structfile = likelyStructure.getValue();
+ }
+ }
}
- if (subVals.has("structfile"))
+ else if (subVals.has("structfile"))
+ {
+ structfile = subVals.get("structfile");
+ }
+ else if (subVals.has("structid"))
+ {
+ structid = subVals.get("structid");
+ }
+ if (structfile != null)
{
Console.info("***** Attaching paeFile '" + paePath + "' to "
+ "structfile=" + subVals.get("structfile"));
EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
paeFile, subVals.getIndex(), subVals.get("structfile"),
- true, false);
+ true, false, paeLabel);
}
- else if (subVals.has("structid"))
+ else if (structid != null)
{
Console.info("***** Attaching paeFile '" + paePath + "' to "
+ "structid=" + subVals.get("structid"));
EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
paeFile, subVals.getIndex(), subVals.get("structid"),
- true, true);
+ true, true, paeLabel);
}
else
{
Console.debug("***** Attaching paeFile '" + paePath
+ "' to sequence index " + subVals.getIndex());
EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subVals.getIndex(), null, false, false);
+ paeFile, subVals.getIndex(), null, false, false,
+ paeLabel);
// required to readjust the height and position of the pAE
// annotation
}
package jalview.bin.argparser;
+import java.util.Arrays;
+import java.util.List;
import java.util.Locale;
+import java.util.stream.Collectors;
public enum Arg
{
NPP.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
SUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
NIL.setOptions(Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION);
- // BOOTSTRAP args are parsed before a full parse of arguments and
- // so are accessible at an earlier stage to (e.g.) set debug log level,
- // provide a props file (that might set log level), run headlessly, read
- // an argfile instead of other args.
+ // Opt.BOOTSTRAP args are parsed (not linked with no SubVals so using a
+ // simplified parser, see jalview.bin.argparser.BootstrapArgs)
+ // before a full parse of arguments and so can be accessible at an earlier
+ // stage to (e.g.) set debug log level, provide a props file (that might set
+ // log level), run headlessly, read an argfile instead of other args.
}
private final String[] argNames;
public String toLongString()
{
StringBuilder sb = new StringBuilder();
- sb.append("Arg: ").append(this.name());
- for (String name : getNames())
- {
- sb.append(", '").append(name).append("'");
- }
- sb.append("\nOptions: ");
- boolean first = true;
- for (Opt o : argOptions)
- {
- if (!first)
- {
- sb.append(", ");
- }
- sb.append(o.toString());
- first = false;
- }
+ sb.append(this.getClass().getName()).append('.').append(this.name());
+ sb.append('(');
+ if (getNames().length > 0)
+ sb.append('"');
+ sb.append(String.join("\", \"", getNames()));
+ if (getNames().length > 0)
+ sb.append('"');
+ sb.append(")\n");
+ sb.append("\nOpt: ");
+ // map List<Opt> to List<String> for the String.join
+ List<String> optList = Arrays.asList(argOptions).stream()
+ .map(opt -> opt.name()).collect(Collectors.toList());
+ sb.append(String.join(", ", optList));
sb.append("\n");
return sb.toString();
}
{
return id;
}
+
+ public SubVals getSubVals()
+ {
+ return ArgParser.getSubVals(getValue());
+ }
}
\ No newline at end of file
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.stream.Collectors;
import jalview.bin.Console;
import jalview.bin.argparser.Arg.Opt;
public class ArgValues
{
- protected static final String ID = "id";
+ public static final String ID = "id";
private Arg arg;
if (arg.hasOption(Opt.STRING))
{
sb.append("Values:");
- boolean first = true;
- for (ArgValue av : argValueList)
- {
- String v = av.getValue();
- if (!first)
- sb.append(",");
- sb.append("\n '");
- sb.append(v).append("'");
- first = false;
- }
+ sb.append("'")
+ .append(String
+ .join("',\n '",
+ argValueList.stream().map(av -> av.getValue())
+ .collect(Collectors.toList())))
+ .append("'");
sb.append("\n");
}
sb.append("Count: ").append(argCount).append("\n");
{
return content;
}
+
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+ if (subVals == null)
+ return "";
+ for (Map.Entry<String, String> m : subVals.entrySet())
+ {
+ sb.append(m.getKey()).append('=').append(m.getValue()).append("\n");
+ }
+ return sb.toString();
+ }
}
\ No newline at end of file
package jalview.datamodel;
-import java.math.BigInteger;
import java.util.ArrayList;
import java.util.List;
-import java.util.Spliterator;
import java.util.StringTokenizer;
import jalview.bin.Console;
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
- for (int c=0;c<cm.getWidth();c++)
+ for (int c = 0; c < cm.getWidth(); c++)
{
- ContactListI cl=cm.getContactList(c);
- if (cl!=null) {
- for (int h=0;h<=cl.getContactHeight();h++)
+ ContactListI cl = cm.getContactList(c);
+ if (cl != null)
{
- if (sb.length()>0) {
- sb.append('\t');
+ for (int h = 0; h <= cl.getContactHeight(); h++)
+ {
+ if (sb.length() > 0)
+ {
+ sb.append('\t');
+ }
+ sb.append(cl.getContactAt(h));
}
- sb.append(cl.getContactAt(h));
- }
}
}
return sb.toString();
int rows)
{
float[][] vals = new float[cols][rows];
- StringTokenizer tabsep = new StringTokenizer(values,""+'\t');
- int c=0,r=0;
-
+ StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
+ int c = 0, r = 0;
+
while (tabsep.hasMoreTokens())
{
double elem = Double.valueOf(tabsep.nextToken());
- vals[c][r++]=(float) elem;
- if (r>=vals[c].length)
+ vals[c][r++] = (float) elem;
+ if (r >= vals[c].length)
{
- r=0;
+ r = 0;
c++;
}
- if (c>=vals.length)
+ if (c >= vals.length)
{
-
+
break;
}
}
if (tabsep.hasMoreElements())
{
- Console.warn("Ignoring additional elements for Float string to contact matrix parsing.");
+ Console.warn(
+ "Ignoring additional elements for Float string to contact matrix parsing.");
}
-
+
return vals;
}
}
String getAnnotLabel();
/**
- * string indicating how the contactMatrix should be rendered - stored in calcId
- * @return
+ * string indicating how the contactMatrix should be rendered - stored in
+ * calcId
+ *
+ * @return
*/
String getType();
int getWidth();
+
int getHeight();
}
public class SeqDistanceContactMatrix implements ContactMatrixI
{
private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
+
private int width = 0;
public SeqDistanceContactMatrix(int width)
{
Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
- null, false, false);
+ null, false, false, null);
if (al.getAlignmentAnnotation() != null)
{
AlignmentI pdbAlignment, String retrievalUrl) throws IOException
{
File pae = fetchAlphaFoldPAE(id, retrievalUrl);
- addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false);
+ addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false, null);
}
public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
- int index, String id, boolean isStruct, boolean isStructId)
+ int index, String id, boolean isStruct, boolean isStructId,
+ String label)
{
FileInputStream paeInput = null;
try
if (ssm != null)
{
String structFilename = isStructId ? ssm.findFileForPDBId(id) : id;
- addPAEToStructure(ssm, structFilename, pae);
+ addPAEToStructure(ssm, structFilename, pae, label);
}
}
try
{
if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
- index, id))
+ index, id, label))
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "' to sequence.");
}
public static void addPAEToStructure(StructureSelectionManager ssm,
- String structFilename, File pae)
+ String structFilename, File pae, String label)
{
FileInputStream paeInput = null;
try
try
{
- if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput))
+ if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput,
+ label))
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "' to structure.");
*/
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input, int index,
- String seqId) throws IOException, ParseException
+ String seqId, String label) throws IOException, ParseException
{
SequenceI sequence = null;
if (seqId == null)
return false;
}
return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
- sequence);
+ sequence, label);
}
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input,
- SequenceI sequence) throws IOException, ParseException
+ SequenceI sequence, String label)
+ throws IOException, ParseException
{
JSONObject paeDict = parseJSONtoPAEContactMatrix(pae_input);
if (paeDict == null)
(Map<String, Object>) paeDict);
AlignmentAnnotation cmannot = sequence.addContactList(matrix);
+ if (label != null)
+ cmannot.label = label;
pdbAlignment.addAnnotation(cmannot);
return true;
}
public static boolean importPaeJSONAsContactMatrixToStructure(
- StructureMapping[] smArray, InputStream paeInput)
+ StructureMapping[] smArray, InputStream paeInput, String label)
throws IOException, ParseException
{
boolean someDone = false;
for (StructureMapping sm : smArray)
{
boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
- paeInput);
+ paeInput, label);
someDone |= thisDone;
}
return someDone;
}
public static boolean importPaeJSONAsContactMatrixToStructure(
- StructureMapping sm, InputStream paeInput)
+ StructureMapping sm, InputStream paeInput, String label)
throws IOException, ParseException
{
JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
(Map<String, Object>) pae_obj);
AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
+ if (label != null)
+ {
+ Console.debug("Setting annotation label to '" + label + "'");
+ cmannot.label = label;
+ }
sm.getSequence().addAlignmentAnnotation(cmannot);
return true;
git://source.jalview.org / jalview.git / commitdiff