: Class UtilPRP

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Class UtilPRP

java.lang.Object
  |
  +--UtilPRP

public class UtilPRP
extends java.lang.Object

Class UtilPRP contains common utility fcts. for string-numeric conversions messages to the three message lines in the bottom page as well as displayURL functionality. This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government and Djamel Medjahed (SAIC-Frederick). As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file.

Version:: $Date: 2002/10/14 20:17:17 $ $Revision: $
Author:: P. Lemkin (NCI), Djamel Medjahed (SAIC), NCI-Frederick, Frederick, MD
See Also:: ProtPlot Home
This work was derived from MAExplorer under the Mozilla 1.1 Open Source Public License by Peter Lemkin of the National Cancer Institute, an agency of the United States Government subject to the limitations noted in the accompanying LEGAL file. See licence info on http://maexplorer.sourceforge.org/

Field Summary

static float defaultFloat
          Default value of float for cvs2f() calls

static int defaultInt
          Default value of int for cvs2i() calls

private java.awt.Color lastBG1
          last foreground, background colors cached

private java.awt.Color lastBG2
          last foreground, background colors cached

private java.awt.Color lastBG3
          last foreground, background colors cached

private java.awt.Color lastBG4
          last foreground, background colors cached

private java.awt.Color lastFG1
          last foreground, background colors cached

private java.awt.Color lastFG2
          last foreground, background colors cached

private java.awt.Color lastFG3
          last foreground, background colors cached

private java.awt.Color lastFG4
          last foreground, background colors cached

static java.lang.String mStatus


static int nStateEntries
          # of (name,value) pairs read from the "protplot.prpstate" file

private int parseDelimChar
          current delim of "name(delim)value" pair

private java.lang.String parseName
          current name of "name=value" pair

private java.lang.String parseValue
          current value of "name=value" pair

private static ProtPlot prp
          instance of ProtPlot

private static ShowScatterPlotPopup spp
          instance of ShowScatterPlotPopup

Constructor Summary

(package private) UtilPRP(ProtPlot prp)
          Util() - constructor

Method Summary

(package private) static int[] bubbleSortIndex(float[] data, int len, boolean ascending)
          bubbleSortIndex() - sort copy of float[0:len-1] data with bubble sort, return index[].

(package private) static int[] bubbleSortIndex(java.lang.String[] data, int len, boolean ascending, boolean ignoreCaseFlag)
          bubbleSortIndex() - sort copy of String[0:len-1] data with bubble sort, return index[].

static java.lang.String chkDirFinalSeparator(java.lang.String sPath, java.lang.String fS)
          chkDirFinalSeparator() - make dir path end in fileSeparator.

boolean copyFile(java.lang.String srcName, java.lang.String dstName, java.lang.String optUpdateMsg, int optEstInputFileLth)
          copyFile() - binary copy of one file or URL toa local file

static java.lang.String cvd2s(double v, int precision)
          cvd2s() - convert double to string with precision # of digits If precision > 0 then limit # of digits in fraction

static java.lang.String cvf2s(float v, int precision)
          cvf2s() - convert float to string with precision # of digits If precision > 0 then limit # of digits in fraction

static double cvs2d(java.lang.String str)
          cvs2d() - convert String to double

static float cvs2f(java.lang.String str)
          cvs2f() - convert String to float

static float cvs2f(java.lang.String str, float defVal)
          cvs2f() - convert String to float

static int cvs2i(java.lang.String str)
          cvs2i() - convert String to int

static int cvs2i(java.lang.String str, int defVal)
          cvs2i() - convert String to int

static long cvs2long(java.lang.String str)
          cvs2long() - convert String to int

(package private) static java.lang.String cvtSpacesToUnderscores(java.lang.String str)
          cvtSpacesToUnderscores() - replace spaces and other illegal file name characters with '_' chars to make file names highly portable.

static java.lang.String cvtUnderscores2Spaces(java.lang.String sInput)
          cvtUnderscores2Spaces() - change underscores to spaces

(package private) static java.lang.String cvtValueToStars(float val, float valMax, int maxStars, boolean rightFillFlag)
          cvtValueToStars() - cvt val in[0:valMax] to "****"+" " string where the maximum # of stars for v==vMax is specified.

(package private) static java.lang.String dateStr()
          dateStr() - return a new Date string of the current day and time

boolean deleteLocalFile(java.lang.String fileName)
          deleteLocalFile() - delete local file.

void displayURL(java.lang.String url)
          displayURL() - Display a file in the system browser.

(package private) float getFloatValFromLine(java.lang.String key, java.util.StringTokenizer parser)
          getFloatValFromLine() - get next line and parse value for key 'name='.

java.lang.String getHelpBaseURL()
          getHelpBaseURL() - get the base URL for HELP based on prp.useLocalDocFlag It will either be the ProtPlot server or the /Doc/ directory

(package private) int getIntValFromLine(java.lang.String key, java.util.StringTokenizer parser)
          getIntValFromLine() - get next line and parse value for key 'name='.

(package private) long getLongValFromLine(java.lang.String key, java.util.StringTokenizer parser)
          getLongValFromLine() - get next line and parse value for key 'name='.

(package private) int getNextInt(java.util.StringTokenizer parser)
          getNextInt() - parse next int from StringTokenizer the integers are separated by ',' or '\n'.

(package private) boolean getNextStrNameValFromLine(java.util.StringTokenizer parser)
          getNextStrNameValFromLine() - get next line and parse 'name=value\n'.

java.lang.String getStateStr()
          getStateStr() - generate a tab-delim ProtPlot State string The format is tab-delimted (name \t value \n) with one entry/line.

(package private) java.lang.String getStrValFromLine(java.lang.String key)
          getStrValFromLine() - parse value for key 'name=value\n'.

(package private) java.lang.String getStrValFromLine(java.lang.String key, java.util.StringTokenizer parser)
          getStrValFromLine() - get line and parse value for key 'name=value\n'.

static boolean isNameInList(java.lang.String[] sList, java.lang.String s)
          isNameInList() - test if String s is in a list of strings sList[].

static int nextZoomMag(int val, int maxVal)
          nextZoomMag() - modulo 1X, 2X, 5X, 10X, 20X, 30X, 40X, 50X,

void popupAlertMsg(java.lang.String msg)
          popupAlertMsg() - popup ALERT message and then timeout.

void popupViewer(java.net.URL urlBase, java.lang.String fileIn, java.lang.String windowName)
          popupViewer() - popup another web browser for the help HTML file.

byte[] readBytesFromURL(java.lang.String srcName, java.lang.String optUpdateMsg)
          readBytesFromURL() - read binary data from URL

(package private) boolean readNamedProteinSet(java.lang.String protSetName, java.lang.String destSetName)
          readNamedProteinSet() - read named protein set file and save it Cluster or Filter Save list.

java.util.Hashtable readState(java.lang.String stateFile)
          readState() - read the ProtPlot State file stateFile

(package private) boolean saveNamedProteinSet(java.lang.String protSetName, java.lang.String srcSetName)
          saveNamedProteinSet() - save the named protein set as a "Set/*.set" file.

java.lang.String setPlotModeName()
          setPlotModeName() - lookup the plot mode name

void setText1(java.lang.String text)
          setText1() - change the text1 msg for the panel.

void setText1(java.lang.String msg, java.awt.Color fg, java.awt.Color bg)
          setText1() - change the text1 field in the panel with fg, bg colors You can save the msg as the title.

void setText2(java.lang.String msg)
          setText2() - change the text2 field in the panel.

void setText2(java.lang.String msg, java.awt.Color fg, java.awt.Color bg)
          setText2() - change the text2 field in the panel with fg, bg colors

void setText3(java.lang.String msg)
          setText3() - change the text3 field in the panel.

void setText3(java.lang.String msg, java.awt.Color fg, java.awt.Color bg)
          setText3() - change the text3 field in the panel with fg, bg colors

void setText4(java.lang.String msg)
          setText4() - change the text4 field in the panel.

void setText4(java.lang.String msg, java.awt.Color fg, java.awt.Color bg)
          setText4() - change the text4 field in the panel with fg, bg colors

void showFeatures(java.lang.String msg2, java.lang.String msg3)
          showFeatures() - print features to txtField2 and txtField3

void showMsg(java.lang.String msg)
          showMsg() - print msg to showStatus() and to txtField1

void showMsg(java.lang.String msg, java.awt.Color fg, java.awt.Color bg)
          showMsg() - print msg to showStatus() and to txtField1

void showMsg1(java.lang.String msg, java.awt.Color fg, java.awt.Color bg)
          showMsg1() - print msg to showStatus() and to txtField1 and change color

void showMsg2(java.lang.String msg2)
          showMsg2() - print msg2 to txtField2

void showMsg2(java.lang.String msg2, java.awt.Color fg, java.awt.Color bg)
          showMsg2() - print msg2 to txtField2 and change color

void showMsg3(java.lang.String msg3)
          showMsg3() - print msg3 to txtField3

void showMsg3(java.lang.String msg3, java.awt.Color fg, java.awt.Color bg)
          showMsg3() - print msg3 to txtField3 ALSO: side effect of setting cursor to WAIT_CURSOR if the (fg,bg) is not (black,white).

void showMsg4(java.lang.String msg4)
          showMsg4() - print msg2 to txtField4

void showMsg4(java.lang.String msg4, java.awt.Color fg, java.awt.Color bg)
          showMsg4() - print msg4 to txtField4 ALSO: side effect of setting cursor to WAIT_CURSOR if the (fg,bg) is not (black,white).

static void sleepMsec(int sleepMsec)
          sleepMsec() - sleep nMsec where nMsec must be >= 0 milliseconds.

(package private) boolean updateProtPlotJarFile()
          updateProtPlotJarFile() - update ProtPlot.jar into program install area.

(package private) boolean updateProtPlotProgram()
          updateProtPlotProgram() - verify that want to update the ProtPlot.jar file from the maexplorer.sourceforge.net server.

(package private) boolean updateProtPlotPRPdatabase()
          updateProtPlotPRPdatabase() - verify that want to update PRP/*.prp files from the current server.

(package private) boolean updateProtPlotPRPfile(int n, java.lang.String prpFname)
          updateProtPlotPRPfile() - update ProtPlot PRP/*.prp files into PRP/ install area.

boolean writeState(java.lang.String stateFile)
          writeState() - write the ProtPlot State into stateFile in the same directory that the project is in.

Methods inherited from class java.lang.Object

, clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, toString, wait, wait, wait

Field Detail

prp

private static ProtPlot prp

instance of ProtPlot

spp

private static ShowScatterPlotPopup spp

instance of ShowScatterPlotPopup

mStatus

public static java.lang.String mStatus

nStateEntries

public static int nStateEntries

# of (name,value) pairs read from the "protplot.prpstate" file

defaultInt

public static int defaultInt

Default value of int for cvs2i() calls

defaultFloat

public static float defaultFloat

Default value of float for cvs2f() calls

parseName

private java.lang.String parseName

current name of "name=value" pair

parseValue

private java.lang.String parseValue

current value of "name=value" pair

parseDelimChar

private int parseDelimChar

current delim of "name(delim)value" pair