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java.lang.Object org.emboss.jemboss.parser.ParseAcd
ACD (Ajax command line definition) file parser.
Field Summary | |
private java.lang.String |
attr
parameter data type |
private Dependent[] |
dep
array of dependent variables |
private java.lang.String |
groupList
String of the groups application belongs to |
private boolean |
isPrimaryGp
true if primary group is defined |
private boolean |
isSecondaryGp
true if secondary group is defined |
private java.util.Vector |
listdefault
default for list or select data type |
private int |
mlist
number of list & selection fields - multiple selection |
private int |
nbool
number of checkbox fields |
private int |
nflist
number of filelist fields |
private int |
nfloat
number of float fields |
private int |
nint
number of integer fields |
private int |
nlist
number of list & selection fields - single selection |
private int |
nrange
number of range fields |
private int |
nsection
number of sections |
private int |
nseqs
number of sequence fields |
private int |
nsubsection
number of subsections |
private int |
ntextf
number of text fields |
private int |
numOfDependents
number of dependent variables |
private int |
numofFields
number of ACD fields |
private int |
numofParams
number of parameters in a field |
private double |
nvalue
double value of a parameter |
private java.lang.String |
primaryGp
primary group |
private java.lang.String |
secondaryGp
secondary group |
private java.lang.String |
svalue
string value of a parameter |
private java.util.Vector |
vappF
vector containing the application fields |
Constructor Summary | |
ParseAcd(java.lang.String acdText,
boolean groups)
The constructor takes the ACD as a string. |
Method Summary | |
protected java.lang.String |
formatHelpText(java.lang.String help)
Limits the length of the line for the help text used in the tool tips. |
double |
getDefaultParamValueDbl(int field)
Return a double default parameter |
java.lang.String |
getDefaultParamValueStr(int field)
Gets a String default parameter. |
Dependent[] |
getDependents()
Gets the dependents associated with the ACD. |
java.lang.String |
getExpectedCPU()
Finds any expected cpu level indicator (low, medium, high) |
int |
getGuiHandleNumber(int field)
Gets the handle for a gui component on the Jemboss form. |
java.lang.String |
getHelpParamValue(int field)
Finds the help parameter in an ACD field. |
java.lang.String |
getInfoParamValue(int field)
Finds the prompt, info or help parameter in an ACD field, in that order. |
java.lang.String[] |
getList(int field)
Used for a list data type to put the list items in a String array. |
java.lang.String |
getListLabel(int field,
int index)
For a list data type determine the appropriate String entry. |
java.util.Vector |
getListOrSelectDefault()
Use this after getList or getSelect to retrieve default |
java.lang.String |
getMaxParam(int field)
Locates the max parameter in a field and returns it as a String. |
java.lang.String |
getMinParam(int field)
Locates the min parameter in a field and returns it as a String. |
int |
getNumBool()
Gets the number of boolean data types in the ACD. |
int |
getNumFileList()
Gets the number of filelist data types in the ACD |
int |
getNumList()
Gets the number of list & selection data types in the ACD, using single list selection |
int |
getNumMList()
Gets the number of list & selection data types in the ACD, using multiple list selection |
int |
getNumNfloat()
Gets the number of float data types in the ACD. |
int |
getNumNint()
Gets the number of int data types in the ACD. |
int |
getNumOfDependents()
Gets the number of dependent parameters in the ACD. |
int |
getNumofFields()
Gets the number of fields in the ACD file. |
int |
getNumofParams(int field)
Gets the number of parameters in a ACD field. |
int |
getNumRange()
|
int |
getNumSection()
Gets the number of sections in the ACD |
int |
getNumSeq()
Gets the number of seqset, seqall & sequence data types in the ACD |
int |
getNumSubsection()
Gets the number of nested sections in the ACD |
int |
getNumTextf()
Gets the number of float, string, seqout, outfile, infile, regexp, codon & featout data types in the ACD. |
java.lang.String |
getOutputSequenceFile(int field)
Gets the name of the output sequence field (seqout). |
java.lang.String |
getParameterAttribute(int field,
int param)
Get a specified parameter attribute. |
double |
getParamValueDbl(int field,
int param)
Gets the double value of a parameter. |
java.lang.String |
getParamValueStr(int field,
int param)
Gets the String value of a parameter. |
java.lang.String[] |
getSelect(int field)
Used for a selection type to put the list items in a String array. |
boolean |
isBatchable()
Finds if the program is identifies as being able to run in a batch queue |
boolean |
isDefaultParamValueStr(int field)
Determine if there is a default parameter in a field of the ACD. |
boolean |
isDependents(java.lang.String attr,
int field,
int numofFields)
Always start by calling isDependents(), which calculates the number of dependents and construct the Dependent array. |
boolean |
isMaxParamValue(int field)
Determine if there is a max parameter in a field of the ACD. |
boolean |
isMinParamValue(int field)
Determine if there is a min parameter in a field of the ACD. |
boolean |
isOptionalParam()
Determine if there is a optional parameter in any field of the ACD. |
boolean |
isOptionalParamValue(int field)
Determine if there is a optional parameter in a field of the ACD. |
boolean |
isOutputFile(int field)
Determine if a field is data type outfile. |
boolean |
isOutputGraph(int field)
Determine if a field is data type graph or xygraph. |
boolean |
isOutputSequence(int field)
Determine if data type of a field is seqout. |
boolean |
isParamValueStr(int field,
int param)
Determine if the value of the parameter is a String. |
int |
parseParam(java.io.BufferedReader in,
java.io.StreamTokenizer st)
Parses a parameter in a ACD field |
private java.lang.String |
resolveVariables(java.util.Vector variables,
java.lang.String svalue)
Used to replace the "variable:" or "var:" shorthand notation in the ACD to the full expression it represent |
private void |
setGuiHandleNumber(java.lang.String dataType,
ApplicationFields appF)
Sets the gui handle depending on the data type. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
private int numofFields
private int numofParams
private java.util.Vector vappF
private java.lang.String svalue
private double nvalue
private java.lang.String attr
private Dependent[] dep
private int numOfDependents
private java.lang.String groupList
private int nsection
private int nsubsection
private int ntextf
private int nint
private int nfloat
private int nbool
private int nseqs
private int nflist
private int nlist
private int mlist
private int nrange
private java.util.Vector listdefault
private boolean isPrimaryGp
private boolean isSecondaryGp
private java.lang.String primaryGp
private java.lang.String secondaryGp
Constructor Detail |
public ParseAcd(java.lang.String acdText, boolean groups)
acdText
- String representation of
the ACD filegroups
- boolean determing whether
just to retieve the groupsMethod Detail |
private java.lang.String resolveVariables(java.util.Vector variables, java.lang.String svalue)
variables
- ApplicationFields of var ACD fieldssvalue
- value to be resolved if necessarypublic int getGuiHandleNumber(int field)
field
- field number in the ACD file
public int getNumTextf()
public int getNumNint()
public int getNumNfloat()
public int getNumBool()
public int getNumSeq()
public int getNumFileList()
public int getNumList()
public int getNumMList()
public int getNumRange()
public int getNumSection()
public int getNumSubsection()
public java.lang.String getParameterAttribute(int field, int param)
field
- field number in the ACD fileparam
- parameter number in that field
public boolean isParamValueStr(int field, int param)
public java.lang.String getParamValueStr(int field, int param)
private void setGuiHandleNumber(java.lang.String dataType, ApplicationFields appF)
dataType
- data typeappF
- application fieldpublic double getParamValueDbl(int field, int param)
public boolean isDefaultParamValueStr(int field)
field
- field number
public double getDefaultParamValueDbl(int field)
field
- field number
public boolean isDependents(java.lang.String attr, int field, int numofFields)
attr
- String name of the attributefield
- field numbernumofFields
- total number of fields
public Dependent[] getDependents()
public int getNumOfDependents()
public java.lang.String getMinParam(int field)
field
- field number
public java.lang.String getMaxParam(int field)
field
- field number
public boolean isMinParamValue(int field)
field
- field number
public boolean isMaxParamValue(int field)
field
- field number
public java.lang.String getInfoParamValue(int field)
field
- field number
public java.lang.String getHelpParamValue(int field)
field
- field number
public boolean isBatchable()
public java.lang.String getExpectedCPU()
protected java.lang.String formatHelpText(java.lang.String help)
help
- help text
public boolean isOptionalParamValue(int field)
field
- field number
public boolean isOutputSequence(int field)
field
- field number
public java.lang.String getOutputSequenceFile(int field)
field
- field number
public boolean isOutputGraph(int field)
field
- field number
public boolean isOutputFile(int field)
field
- field number
public java.lang.String getDefaultParamValueStr(int field)
field
- field number
public java.lang.String[] getList(int field)
field
- field number
public java.lang.String getListLabel(int field, int index)
field
- field numberindex
- index into the list
public java.lang.String[] getSelect(int field)
field
- field number
public java.util.Vector getListOrSelectDefault()
public boolean isOptionalParam()
public int getNumofFields()
public int getNumofParams(int field)
field
- field number
public int parseParam(java.io.BufferedReader in, java.io.StreamTokenizer st) throws java.io.IOException
in
- BufferedReaderst
- tokenizer
java.io.IOException
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