error.implementation_error_vamsas_doc_class_should_bind_to_type = Implementation Error: Vamsas Document Class {0} should bind to a {1} (found a {2})
error.invalid_vamsas_rangetype_cannot_resolve_lists = Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!
error.implementation_error_maplist_is_null = Implementation error. MapList is null for initMapType.
-error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key
error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor
error.implementation_error_cannot_map_alignment_sequences = IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.
error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null'
error.implementation_error_vamsas_doc_class_should_bind_to_type = Error de implementación: la clase de documento VAMSAS {0} debe enlazar a {1} (pero se ha encontrado que lo está a {2})
error.invalid_vamsas_rangetype_cannot_resolve_lists = RangeType VAMSAS no válido - ¡no es posible resolver ambas listas de Pos y Seg con los valores elegidos!
error.implementation_error_maplist_is_null = Error de implementación. MapList es nulo en initMapType.
-error.implementation_error_cannot_have_null_alignment = Error de implementación: no es posible tener una clave nula en el alineamiento
error.implementation_error_null_fileparse = Error de implementación. FileParse nulo en el construictor de copia
error.implementation_error_cannot_map_alignment_sequences = Error de implementación: no es posible maper un alineamiento de secuencias desde distintos conjuntos de datos en un único alineamiento en el documento VAMSAS.
error.implementation_error_structure_selection_manager_null = Error de implementación. El contexto structure selection manager's es nulo
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
}
else if (source == alProperties)
{
- StringBuffer contents = new jalview.io.AlignmentProperties(
+ StringBuilder contents = new AlignmentProperties(
viewport.getAlignment()).formatAsString();
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
cap.setText(contents.toString());
import java.util.Arrays;
import java.util.Collections;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.HashSet;
-import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
HiddenColumns hiddenCols;
- public Hashtable alignmentProperties;
+ public Map<Object, Object> alignmentProperties;
private List<AlignedCodonFrame> codonFrameList;
{
if (alignmentProperties == null)
{
- alignmentProperties = new Hashtable();
+ alignmentProperties = new HashMap<>();
}
alignmentProperties.put(key, value);
}
@Override
- public Hashtable getProperties()
+ public Map<Object, Object> getProperties()
{
return alignmentProperties;
}
{
// we really can't do very much here - just try to concatenate strings
// where property collisions occur.
- Enumeration key = toappend.getProperties().keys();
- while (key.hasMoreElements())
+ Iterator<Object> key = toappend.getProperties().keySet().iterator();
+ while (key.hasNext())
{
- Object k = key.nextElement();
+ Object k = key.next();
Object ourval = this.getProperty(k);
Object toapprop = toappend.getProperty(k);
if (ourval != null)
*/
package jalview.datamodel;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Set;
*
* @return hashtable of alignment properties (or null if none are defined)
*/
- Hashtable getProperties();
+ Map<Object, Object> getProperties();
/**
* add a reference to a frame of aligned codons for this alignment
public void alignmentProperties()
{
CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
- StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
+ StringBuilder contents = new AlignmentProperties(
+ viewport.getAlignment())
.formatAsHtml();
cap.setText("<html>" + contents.toString() + "</html>");
}
if (jal.getProperties() != null)
{
- Enumeration en = jal.getProperties().keys();
- while (en.hasMoreElements())
+ for (Entry<Object, Object> prop : jal.getProperties().entrySet())
{
- String key = en.nextElement().toString();
+ String key = prop.getKey().toString();
SequenceSetProperties ssp = new SequenceSetProperties();
ssp.setKey(key);
- ssp.setValue(jal.getProperties().get(key).toString());
+ ssp.setValue(prop.getValue().toString());
vamsasSet.addSequenceSetProperties(ssp);
}
}
if (this.frefedSequence == null)
{
- frefedSequence = new Vector<SeqFref>();
+ frefedSequence = new Vector<>();
}
viewportsAdded.clear();
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.Vector;
/**
/**
* Properties to be added to generated alignment object
*/
- private Hashtable properties;
+ private Map<String, String> properties;
long start;
*/
public void addProperties(AlignmentI al)
{
- if (properties != null && properties.size() > 0)
+ if (properties != null)
{
- Enumeration keys = properties.keys();
- Enumeration vals = properties.elements();
- while (keys.hasMoreElements())
+ for (Entry<String, String> prop : properties.entrySet())
{
- al.setProperty(keys.nextElement(), vals.nextElement());
+ al.setProperty(prop.getKey(), prop.getValue());
}
}
}
* @param value
* - non-null value
*/
- protected void setAlignmentProperty(Object key, Object value)
+ protected void setAlignmentProperty(String key, String value)
{
if (key == null)
{
- throw new Error(MessageManager.getString(
- "error.implementation_error_cannot_have_null_alignment"));
+ throw new Error(
+ "Implementation error: Cannot have null alignment property key.");
}
if (value == null)
{
}
if (properties == null)
{
- properties = new Hashtable();
+ properties = new Hashtable<>();
}
properties.put(key, value);
}
- protected Object getAlignmentProperty(Object key)
+ protected String getAlignmentProperty(String key)
{
if (properties != null && key != null)
{
*/
protected void initData()
{
- seqs = new Vector<SequenceI>();
- annotations = new Vector<AlignmentAnnotation>();
- seqGroups = new ArrayList<SequenceGroup>();
+ seqs = new Vector<>();
+ annotations = new Vector<>();
+ seqGroups = new ArrayList<>();
parseCalled = false;
}
@Override
public void setSeqs(SequenceI[] s)
{
- seqs = new Vector<SequenceI>();
+ seqs = new Vector<>();
for (int i = 0; i < s.length; i++)
{
{
if (newickStrings == null)
{
- newickStrings = new Vector<String[]>();
+ newickStrings = new Vector<>();
}
newickStrings.addElement(new String[] { treeName, newickString });
}
*/
package jalview.io;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import java.io.PrintWriter;
-import java.io.StringWriter;
-import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.Map;
/**
* Render associated attributes of an alignment. The heart of this code was
*/
public class AlignmentProperties
{
+ private static final String BR_TAG = "<br>";
+ private static final String NEWLINE = System.getProperty("line.separator");
AlignmentI alignment;
public AlignmentProperties(AlignmentI alignment)
/**
* render the alignment's properties report as text or an HTML fragment
*
- * @param pw
* @param html
*/
- protected void writeProperties(PrintWriter pw, boolean html)
+ protected StringBuilder writeProperties(boolean html)
{
- final String nl = html ? "<br>" : System.getProperty("line.separator");
+ StringBuilder sb = new StringBuilder(256);
+ final String nl = html ? BR_TAG : NEWLINE;
float avg = 0;
int min = Integer.MAX_VALUE, max = 0;
for (int i = 0; i < alignment.getHeight(); i++)
}
}
avg = avg / alignment.getHeight();
- pw.print(nl);
- pw.print("Sequences: " + alignment.getHeight());
- pw.print(nl);
- pw.print("Minimum Sequence Length: " + min);
- pw.print(nl);
- pw.print("Maximum Sequence Length: " + max);
- pw.print(nl);
- pw.print("Average Length: " + (int) avg);
+ sb.append(nl);
+ sb.append("Sequences: " + alignment.getHeight());
+ sb.append(nl);
+ sb.append("Minimum Sequence Length: " + min);
+ sb.append(nl);
+ sb.append("Maximum Sequence Length: " + max);
+ sb.append(nl);
+ sb.append("Average Length: " + (int) avg);
- if (((Alignment) alignment).alignmentProperties != null)
+ Map<Object, Object> props = alignment.getProperties();
+ if (props != null && !props.isEmpty())
{
- pw.print(nl);
- pw.print(nl);
+ sb.append(nl);
+ sb.append(nl);
if (html)
{
- pw.print("<table border=\"1\">");
+ sb.append("<table border=\"1\">");
}
- Hashtable props = ((Alignment) alignment).alignmentProperties;
- Enumeration en = props.keys();
- while (en.hasMoreElements())
+
+ /*
+ * sort keys alphabetically for ease of reading the output
+ */
+ Object[] keys = props.keySet().toArray(new Object[props.size()]);
+ Arrays.sort(keys, new Comparator<Object>()
{
- String key = en.nextElement().toString();
- String vals = props.get(key).toString();
- if (html)
+ @Override
+ public int compare(Object o1, Object o2)
{
- // wrap the text in the table
- StringBuffer val = new StringBuffer();
- int pos = 0, npos;
- do
- {
- npos = vals.indexOf("\n", pos);
- if (npos == -1)
- {
- val.append(vals.substring(pos));
- }
- else
- {
- val.append(vals.substring(pos, npos));
- val.append("<br>");
- }
- pos = npos + 1;
- } while (npos != -1);
- pw.print("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
+ return String.CASE_INSENSITIVE_ORDER.compare(o1.toString(),
+ o2.toString());
}
- else
+ });
+ for (Object key : keys)
+ {
+ String value = props.get(key).toString();
+ if (html)
{
- pw.print(nl + key + "\t" + vals);
+ value = value.replaceAll("\\R", value); // Java 8 newline matcher
+ value = formatHrefs(value);
}
+ appendRow(sb, key.toString(), value, html);
}
if (html)
{
- pw.print("</table>");
+ sb.append("</table>");
}
}
+ return sb;
}
/**
- * generate a report as plain text
+ * Helper method to change any token starting with http into an html href
*
+ * @param value
* @return
*/
- public StringBuffer formatAsString()
+ private String formatHrefs(String value)
+ {
+ if (!value.contains("http"))
+ {
+ return value;
+ }
+
+ StringBuilder sb = new StringBuilder(value.length() * 3);
+ String[] tokens = value.split("\\s");
+ boolean found = false;
+ boolean first = true;
+ for (String token : tokens)
+ {
+ if (token.startsWith("http"))
+ {
+ token = "<a href=\"" + token + "\">" + token + "</a>";
+ found = true;
+ }
+ if (!first)
+ {
+ sb.append(" ");
+ }
+ sb.append(token);
+ first = false;
+ }
+ return found ? sb.toString() : value;
+ }
+
+ /**
+ * A helper method to add one key-value row, optionally in HTML table entry
+ * format
+ *
+ * @param sb
+ * @param key
+ * @param value
+ * @param html
+ */
+ private void appendRow(StringBuilder sb, String key, String value,
+ boolean html)
{
- return formatReport(false);
+ if (html)
+ {
+ sb.append("<tr><td>").append(key).append("</td><td>").append(value)
+ .append("</td></tr>");
+ }
+ else
+ {
+ sb.append(html ? BR_TAG : NEWLINE).append(key).append("\t")
+ .append(value);
+ }
}
- protected StringBuffer formatReport(boolean html)
+ /**
+ * generate a report as plain text
+ *
+ * @return
+ */
+ public StringBuilder formatAsString()
{
- StringWriter content = new StringWriter();
- writeProperties(new PrintWriter(content), html);
- return content.getBuffer();
+ return writeProperties(false);
}
/**
*
* @return
*/
- public StringBuffer formatAsHtml()
+ public StringBuilder formatAsHtml()
{
- return formatReport(true);
+ return writeProperties(true);
}
}
* @return annotation file
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
- List<SequenceGroup> list, Hashtable properties, HiddenColumns cs,
- AlignmentI al, ViewDef view)
+ List<SequenceGroup> list, Map<Object, Object> properties,
+ HiddenColumns cs, AlignmentI al, ViewDef view)
{
if (view != null)
{
text.append(newline);
text.append(newline);
text.append("ALIGNMENT");
- Enumeration en = properties.keys();
- while (en.hasMoreElements())
+ for (Object ko : properties.keySet())
{
- String key = en.nextElement().toString();
+ String key = ko.toString();
text.append("\t");
text.append(key);
text.append("=");
- text.append(properties.get(key));
+ text.append(properties.get(ko));
}
// TODO: output alignment visualization settings here if required
// iterate through one or more views, defining, marking columns and rows
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Vector;
import com.stevesoft.pat.Regex;
String version;
// String id;
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
+ LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
Regex p, r, rend, s, x;
// Temporary line for processing RNA annotation
// String RNAannot = "";
strucAnn = new Hashtable();
}
- Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+ Vector<AlignmentAnnotation> newStruc = new Vector<>();
parseAnnotationRow(newStruc, type, ns);
for (AlignmentAnnotation alan : newStruc)
{
private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
{
DBRefEntry dbrf = null;
- List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> dbrs = new ArrayList<>();
String seqdb = "Unknown", sdbac = "" + dbr;
int st = -1, en = -1, p;
if ((st = sdbac.indexOf("/")) > -1)
// output database type
if (al.getProperties() != null)
{
- if (!al.getProperties().isEmpty())
+ for (Entry<Object, Object> prop : al.getProperties().entrySet())
{
- Enumeration key = al.getProperties().keys();
- Enumeration val = al.getProperties().elements();
- while (key.hasMoreElements())
- {
- out.append("#=GF " + key.nextElement() + " " + val.nextElement());
- out.append(newline);
- }
+ out.append("#=GF " + prop.getKey().toString() + " "
+ + prop.getValue().toString());
+ out.append(newline);
}
}
git://source.jalview.org / jalview.git / commitdiff