label.removed_empty_columns = Removed {0} empty columns.
label.paste_newick_tree_file = Paste your Newick tree file here.
label.order_by_params = Order by {0}
-label.html_content = <html>{0}</html>
label.paste_pdb_file= Paste your PDB file here.
label.paste_pdb_file_for_sequence = Paste PDB file for sequence {0}
label.could_not_parse_newick_file = Could not parse Newick file\!\n {0}
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_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key
+error.implementation_error_maplist_is_null = Implementation error. MapList is null for initMapType.
error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor
error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null'
exception.ssm_context_is_null = SSM context is null
label.removed_empty_columns = {0} columnas vacías eliminadas.
label.paste_newick_tree_file = Pegar su fichero árbol Newick aquí.
label.order_by_params = Ordenar por {0}
-label.html_content = <html>{0}</html>
label.paste_pdb_file= Pegar tu fichero PDB aquí.
label.paste_pdb_file_for_sequence = Pegar fichero PDB para la secuencia {0}
label.could_not_parse_newick_file = No se pudo analizar el fichero Newick\!\n {0}
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_cannot_have_null_alignment = Error de implementación: no es posible tener una clave nula en el alineamiento
+error.implementation_error_maplist_is_null = Error de implementación. MapList es nulo en initMapType.
error.implementation_error_null_fileparse = Error de implementación. FileParse nulo en el construictor de copia
error.implementation_error_structure_selection_manager_null = Error de implementación. El contexto structure selection manager's es nulo
exception.ssm_context_is_null = El contexto SSM es nulo
? sequences[0].getDisplayId(true)
: "Selection"),
600, 500);
- cap.setText(
- MessageManager.formatMessage("label.html_content", new Object[]
- { contents.toString() }));
+ cap.setText("<html>" + contents.toString() + "</html>");
}
void editName()
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.BitSet;
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;
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
}
@Override
- public void alignmentProperties()
- {
- JComponent pane;
- StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
-
- .formatAsHtml();
- String content = MessageManager.formatMessage("label.html_content",
- new Object[]
- { contents.toString() });
- contents = null;
-
- if (Platform.isJS())
- {
- JLabel textLabel = new JLabel();
- textLabel.setText(content);
- textLabel.setBackground(Color.WHITE);
-
- pane = new JPanel(new BorderLayout());
- ((JPanel) pane).setOpaque(true);
- pane.setBackground(Color.WHITE);
- ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
- }
- else
- /**
- * Java only
- *
- * @j2sIgnore
- */
- {
- JEditorPane editPane = new JEditorPane("text/html", "");
- editPane.setEditable(false);
- editPane.setText(content);
- pane = editPane;
- }
-
- JInternalFrame frame = new JInternalFrame();
-
- frame.getContentPane().add(new JScrollPane(pane));
-
- Desktop.addInternalFrame(frame, MessageManager
- .formatMessage("label.alignment_properties", new Object[]
- { getTitle() }), 500, 400);
- }
+ public void alignmentProperties() {
+ JComponent pane;
+ StringBuilder contents = new StringBuilder(128);
+ contents.append("<html><body>");
+ contents.append(new AlignmentProperties(viewport.getAlignment()).formatAsHtml());
+ contents.append("</body></html>");
+
+ String content = contents.toString();
+
+ JInternalFrame frame = null;
+ if (Platform.isJS()) {
+ JLabel textLabel = new JLabel();
+ textLabel.setText(content);
+ textLabel.setBackground(Color.WHITE);
+
+ pane = new JPanel(new BorderLayout());
+ ((JPanel) pane).setOpaque(true);
+ pane.setBackground(Color.WHITE);
+ ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
+ frame = new JInternalFrame();
+ frame.getContentPane().add(new JScrollPane(pane));
+ } else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ cap.setText(content);
+ frame = cap;
+ }
+
+ Desktop.addInternalFrame(frame,
+ MessageManager.formatMessage("label.alignment_properties", new Object[] { getTitle() }), 500, 400);
+ }
/**
* DOCUMENT ME!
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;
import jalview.datamodel.AlignmentAnnotation;
/**
* 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 jalview.datamodel.SequenceI;
-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");
+
+ private static final String PCT_FORMAT = "%.1f%%";
+
AlignmentI alignment;
public AlignmentProperties(AlignmentI alignment)
/**
* render the alignment's properties report as text or an HTML fragment
*
- * @param pw
* @param html
*/
- public void writeProperties(PrintWriter pw, boolean html)
+ protected StringBuilder writeProperties(boolean html)
{
- final String nl = html ? "<br>" : System.getProperty("line.separator");
- float avg = 0;
- int min = Integer.MAX_VALUE, max = 0;
- for (int i = 0; i < alignment.getHeight(); i++)
+ StringBuilder sb = new StringBuilder(256);
+ final String nl = html ? BR_TAG : NEWLINE;
+ int totalLength = 0;
+ int totalGaps = 0;
+ int minLength = Integer.MAX_VALUE;
+ int maxLength = 0;
+ float maxUngapped = 0f;
+ float minUngapped = Float.MAX_VALUE;
+
+ final int height = alignment.getHeight();
+ final int width = alignment.getWidth();
+
+ for (int i = 0; i < height; i++)
{
- int size = 1 + alignment.getSequenceAt(i).getEnd()
- - alignment.getSequenceAt(i).getStart();
- avg += size;
- if (size > max)
- {
- max = size;
- }
- if (size < min)
- {
- min = size;
- }
+ SequenceI seq = alignment.getSequenceAt(i);
+ // sequence length including gaps:
+ int seqWidth = seq.getLength();
+ // sequence length excluding gaps:
+ int seqLength = 1 + seq.getEnd() - seq.getStart();
+ int gapCount = seqWidth - seqLength; // includes padding
+ totalLength += seqLength;
+ totalGaps += gapCount;
+ maxLength = Math.max(maxLength, seqLength);
+ minLength = Math.min(minLength, seqLength);
+
+ /*
+ * proportion of aligned sequence that is ungapped
+ * (note: normalised by alignment width here)
+ */
+ float ungapped = (seqWidth - gapCount) / (float) seqWidth;
+ maxUngapped = Math.max(maxUngapped, ungapped);
+ minUngapped = Math.min(minUngapped, ungapped);
}
- 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);
-
- if (((Alignment) alignment).alignmentProperties != null)
+ float avgLength = totalLength / (float) height;
+
+ sb.append(html ? "<table border=\"1\">" : nl);
+ appendRow(sb, "Sequences", String.valueOf(height), html);
+ appendRow(sb, "Alignment width", String.valueOf(width),
+ html);
+ appendRow(sb, "Minimum Sequence Length", String.valueOf(minLength),
+ html);
+ appendRow(sb, "Maximum Sequence Length", String.valueOf(maxLength),
+ html);
+ appendRow(sb, "Average Length", String.valueOf((int) avgLength), html);
+ appendRow(sb, "Minimum (sequence length / width)",
+ String.format(PCT_FORMAT, minUngapped * 100f), html);
+ appendRow(sb, "Maximum (sequence length / width)",
+ String.format(PCT_FORMAT, maxUngapped * 100f), html);
+ appendRow(sb, "Residue density", String.format(PCT_FORMAT,
+ (height * width - totalGaps) * 100f / (height * width)), html);
+ appendRow(sb, "Gap density",
+ String.format(PCT_FORMAT, totalGaps * 100f / (height * width)),
+ html);
+ sb.append(html ? "</table>" : nl);
+
+ 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;
// 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);
}
}
label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));
label.setOpaque(false);
label.setPreferredSize(new Dimension(260, 34));
- label.setText(
- MessageManager.formatMessage("label.html_content", new String[]
- { MessageManager.getString(
- "label.save_colour_scheme_with_unique_name_added_to_colour_menu") }));
+ label.setText("<html>" + MessageManager.getString(
+ "label.save_colour_scheme_with_unique_name_added_to_colour_menu")
+ + "</html>");
caseSensitive.setText(MessageManager.getString("label.case_sensitive"));
caseSensitive.addActionListener(new ActionListener()
{
{ choosers[0] });
}
- selectedButtons = new ArrayList<JButton>();
+ selectedButtons = new ArrayList<>();
}
/**
}
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);
vamsasSet.getSequenceSetProperties().add(ssp);
}
--- /dev/null
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.testng.annotations.Test;
+
+public class AlignmentPropertiesTest
+{
+ @Test(groups="Functional")
+ public void testWriteProperties_asHtml()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "--ABC-DEFGH-"); // 8 residues
+ SequenceI seq2 = new Sequence("Seq2", "---BC-DE-KH-"); // 6
+ SequenceI seq3 = new Sequence("Seq3", "-RABCFDE-KH-"); // 9
+ AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+ AlignmentProperties ap = new AlignmentProperties(al);
+ StringBuilder sb = ap.writeProperties(true);
+ String expected = "<table border=\"1\">"
+ + "<tr><td>Sequences</td><td>3</td></tr>"
+ + "<tr><td>Alignment width</td><td>12</td></tr>"
+ + "<tr><td>Minimum Sequence Length</td><td>6</td></tr>"
+ + "<tr><td>Maximum Sequence Length</td><td>9</td></tr>"
+ + "<tr><td>Average Length</td><td>7</td></tr>"
+ + "<tr><td>Minimum (sequence length / width)</td><td>50.0%</td></tr>" // 6/12
+ + "<tr><td>Maximum (sequence length / width)</td><td>75.0%</td></tr>" // 9/12
+ + "<tr><td>Residue density</td><td>63.9%</td></tr>" // 23/36
+ + "<tr><td>Gap density</td><td>36.1%</td></tr>" + "</table>";
+ assertEquals(sb.toString(), expected);
+ }
+}
git://source.jalview.org / jalview.git / commitdiff